From colin.hawco at mail.mcgill.ca Tue Apr 2 12:10:30 2013 From: colin.hawco at mail.mcgill.ca (Colin Shaun Hawco, M) Date: Tue, 2 Apr 2013 16:10:30 +0000 Subject: [MINC-users] mincreeample transformation problem Message-ID: Hello all, I am having a problem with mincresample for a single participant in my study. I am attempting to normalize EPI data into MNI space. My basic pipeline is something like this: calculate transform, high-res T1 to MNi space (mincANTS) calculate transform, EPI to T1 (to account for any movement between scans, mritoself) concat transform I then apply the transform, using mincresample. Because I am analyzing my data in SPM, I am transforming it into the same space/voxel size as the SPM-EPI template (this has several advantages for me). So my command is, paraphrased: mincresample -like EPI_templace.mnc -transform epi2mni.xfm epi.mnc epi_normalized.mnc This works very well on all my data sets, save one. In one case, i was unable to do the T1 scan due to time constraints (technical problems delayed the scan). However, I was able to get a T1 scan from a different day from this participant. But my pipline fails, and when I apply the transform, the EPI image is shifted, such that the actual data is being partially moved outside the range of the file. I attached an image to show what I mean. Upon further investigation, it seems the transforms themselves are not to blame. the problem is when I run mincresample and use the EPI_template.mnc. So, for example, if I do this, I get what looks like a good reg, but the data has the wrong voxel size and dimensions: mincresample -like epi_file.mnc -transform epi2mni.xfm epi_file.mnc epi_normalized.mnc In this case, when I do -like the file I am transforming, the data is not shifted out of range, and appears to overlay on the MNI152 brain. But as soon as I do -like EPI_template.mnc, things go wrong, and the data is majorly shifted in the range of the file, and the registration with the MNI brain is garbage. This was a complex and challenging study, with only 16 usable data sets (counting this one), so i would really like to recover this data. Does anyone have any idea why I could be having this problem? I supect there is some confusion over transforming the origin, but I am not sophisticated with minctools enough to figure it out. Also, I'd like to emphasize, the pipeline works on all 15 other participants. I really appreciate any help. Colin Hawco, PhD Post Doctoral Researcher Temerty Centre for Therapeutic Brain Intervention Centre for Addiction and Mental Health (CAMH) University of Toronto "Disorder Expands" From vladimir.fonov at gmail.com Tue Apr 2 12:15:37 2013 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Tue, 02 Apr 2013 12:15:37 -0400 Subject: [MINC-users] mincreeample transformation problem In-Reply-To: References: Message-ID: <515B0429.2060805@gmail.com> Hello, I think your attachment didn't go through - can you post it online somewhere. Also, can you post output of mincheader on both T1w and EPI files that cause problems? On 13-04-02 12:10 PM, Colin Shaun Hawco, M wrote: > Hello all, > > I am having a problem with mincresample for a single participant in my study. I am attempting to normalize EPI data into MNI space. My basic pipeline is something like this: > > calculate transform, high-res T1 to MNi space (mincANTS) > calculate transform, EPI to T1 (to account for any movement between scans, mritoself) > concat transform > > I then apply the transform, using mincresample. Because I am analyzing my data in SPM, I am transforming it into the same space/voxel size as the SPM-EPI template (this has several advantages for me). So my command is, paraphrased: > > mincresample -like EPI_templace.mnc -transform epi2mni.xfm epi.mnc epi_normalized.mnc > > This works very well on all my data sets, save one. > > In one case, i was unable to do the T1 scan due to time constraints (technical problems delayed the scan). However, I was able to get a T1 scan from a different day from this participant. But my pipline fails, and when I apply the transform, the EPI image is shifted, such that the actual data is being partially moved outside the range of the file. I attached an image to show what I mean. > > Upon further investigation, it seems the transforms themselves are not to blame. the problem is when I run mincresample and use the EPI_template.mnc. So, for example, if I do this, I get what looks like a good reg, but the data has the wrong voxel size and dimensions: > > mincresample -like epi_file.mnc -transform epi2mni.xfm epi_file.mnc epi_normalized.mnc > > In this case, when I do -like the file I am transforming, the data is not shifted out of range, and appears to overlay on the MNI152 brain. But as soon as I do -like EPI_template.mnc, things go wrong, and the data is majorly shifted in the range of the file, and the registration with the MNI brain is garbage. > > This was a complex and challenging study, with only 16 usable data sets (counting this one), so i would really like to recover this data. Does anyone have any idea why I could be having this problem? I supect there is some confusion over transforming the origin, but I am not sophisticated with minctools enough to figure it out. Also, I'd like to emphasize, the pipeline works on all 15 other participants. > > I really appreciate any help. -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From a.janke at gmail.com Tue Apr 2 18:26:01 2013 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 3 Apr 2013 08:26:01 +1000 Subject: [MINC-users] mincreeample transformation problem In-Reply-To: References: Message-ID: Hi Colin, As Vladimir mentioned the attachment didn't come through (they aren't allowed with this list). However my guess would be that one of your files for this patient has irregular sampling. A mincheader on all the files involved for this patient will let you know if this is the case. a On 3 April 2013 02:10, Colin Shaun Hawco, M wrote: > mincresample -like EPI_templace.mnc -transform epi2mni.xfm epi.mnc epi_normalized.mnc > > This works very well on all my data sets, save one. > > In one case, i was unable to do the T1 scan due to time constraints (technical problems delayed the scan). However, I was able to get a T1 scan from a different day from this participant. But my pipline fails, and when I apply the transform, the EPI image is shifted, such that the actual data is being partially moved outside the range of the file. I attached an image to show what I mean. > > Upon further investigation, it seems the transforms themselves are not to blame. the problem is when I run mincresample and use the EPI_template.mnc. So, for example, if I do this, I get what looks like a good reg, but the data has the wrong voxel size and dimensions: > > mincresample -like epi_file.mnc -transform epi2mni.xfm epi_file.mnc epi_normalized.mnc > > In this case, when I do -like the file I am transforming, the data is not shifted out of range, and appears to overlay on the MNI152 brain. But as soon as I do -like EPI_template.mnc, things go wrong, and the data is majorly shifted in the range of the file, and the registration with the MNI brain is garbage. > > This was a complex and challenging study, with only 16 usable data sets (counting this one), so i would really like to recover this data. Does anyone have any idea why I could be having this problem? I supect there is some confusion over transforming the origin, but I am not sophisticated with minctools enough to figure it out. Also, I'd like to emphasize, the pipeline works on all 15 other participants. From colin.hawco at mail.mcgill.ca Wed Apr 3 12:40:19 2013 From: colin.hawco at mail.mcgill.ca (Colin Shaun Hawco, M) Date: Wed, 3 Apr 2013 16:40:19 +0000 Subject: [MINC-users] mincreeample transformation problem In-Reply-To: References: Message-ID: Thanks for the replies, The attached file just showed an axial slice of EPI, with the data shirted forward such that the front of the brain is cut off by the edge of the image. Because of the size of the mincheaders, i need to split up the message. T1 image netcdf p121_anat { dimensions: xspace = 160 ; zspace = 256 ; yspace = 256 ; variables: double xspace(xspace) ; xspace:varid = "MINC standard variable" ; xspace:vartype = "dimension____" ; xspace:version = "MINC Version 1.0" ; xspace:comments = "X increases from patient left to right" ; xspace:spacing = "regular__" ; xspace:alignment = "centre" ; xspace:step = 1. ; xspace:start = -74.777108669281 ; xspace:spacetype = "native____" ; xspace:direction_cosines = 1., -0., 0. ; int zspace ; zspace:varid = "MINC standard variable" ; zspace:vartype = "dimension____" ; zspace:version = "MINC Version 1.0" ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:step = -1. ; zspace:start = 125.30120491982 ; zspace:spacetype = "native____" ; zspace:direction_cosines = 0., 0., 1. ; int yspace ; yspace:varid = "MINC standard variable" ; yspace:vartype = "dimension____" ; yspace:version = "MINC Version 1.0" ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:step = -1. ; yspace:start = 167.1325302124 ; yspace:spacetype = "native____" ; yspace:direction_cosines = 0., 1., -0. ; short image(xspace, zspace, yspace) ; image:parent = "rootvariable" ; image:varid = "MINC standard variable" ; image:vartype = "group________" ; image:version = "MINC Version 1.0" ; image:signtype = "signed__" ; image:valid_range = 0., 4095. ; image:complete = "true_" ; image:image-min = "--->image-min" ; image:image-max = "--->image-max" ; int rootvariable ; rootvariable:varid = "MINC standard variable" ; rootvariable:vartype = "group________" ; rootvariable:version = "MINC Version 1.0" ; rootvariable:parent = "" ; rootvariable:children = "image\n", "patient\n", "study\n", "acquisition\n", "dicominfo\n", "dicom_groups" ; double image-min(xspace) ; image-min:varid = "MINC standard variable" ; image-min:vartype = "var_attribute" ; image-min:version = "MINC Version 1.0" ; image-min:_FillValue = 0. ; image-min:parent = "image" ; double image-max(xspace) ; image-max:varid = "MINC standard variable" ; image-max:vartype = "var_attribute" ; image-max:version = "MINC Version 1.0" ; image-max:_FillValue = 1. ; image-max:parent = "image" ; int patient ; patient:parent = "rootvariable" ; patient:varid = "MINC standard variable" ; patient:vartype = "group________" ; patient:version = "MINC Version 1.0" ; patient:full_name = "pt121" ; patient:identification = "09.03.27-10:18:12-DST-1.3.12.2.1107.5.2.14.16505" ; patient:birthdate = "19830703" ; patient:age = "025Y" ; patient:sex = "female" ; patient:weight = 57. ; int study ; study:parent = "rootvariable" ; study:varid = "MINC standard variable" ; study:vartype = "group________" ; study:version = "MINC Version 1.0" ; study:start_date = "20090327" ; study:start_time = "101814.640000 " ; study:modality = "MRI__" ; study:manufacturer = "SIEMENS " ; study:model = "SonataVision" ; study:field_value = 1.5 ; study:software_version = "syngo MR A30 4VA30A " ; study:serial_no = "16505 " ; study:calibration_date = "20050630" ; study:institution = "McConnell Brain Imaging Center" ; study:station_id = "MRC " ; study:performing_physician = "" ; study:operator = "lm" ; study:procedure = "FUNCTIONAL^Dr Lepage" ; study:study_id = "20090328.101814" ; int acquisition ; acquisition:parent = "rootvariable" ; acquisition:varid = "MINC standard variable" ; acquisition:vartype = "group________" ; acquisition:version = "MINC Version 1.0" ; acquisition:acquisition_id = "4" ; acquisition:start_time = "20090327 101814.640000 " ; acquisition:scanning_sequence = "*fl3d1_ns " ; acquisition:protocol_name = "GLOBAL_no angulation" ; acquisition:receive_coil = "CP_HeadArray" ; acquisition:transmit_coil = "Body" ; acquisition:repetition_time = 0.022 ; acquisition:echo_time = 0.0092 ; acquisition:echo_number = 0. ; acquisition:flip_angle = 30. ; acquisition:slice_thickness = 1. ; acquisition:num_slices = 1. ; acquisition:num_dyn_scans = 1. ; acquisition:num_averages = 1. ; acquisition:imaging_frequency = 63687939. ; acquisition:imaged_nucleus = "1H" ; acquisition:window_center = 46. ; acquisition:window_width = 135. ; acquisition:num_phase_enc_steps = 256. ; acquisition:percent_sampling = 10000. ; acquisition:percent_phase_fov = 10000. ; acquisition:pixel_bandwidth = 70. ; acquisition:phase_enc_dir = "ROW" ; acquisition:SAR = 0.03627666831017 ; acquisition:mr_acq_type = "3D" ; acquisition:image_type = "ORIGINAL\\PRIMARY\\M\\ND " ; acquisition:MrProt_dump = "disabled" ; int dicominfo ; dicominfo:vartype = "group________" ; dicominfo:varid = "MNI DICOM information variable" ; dicominfo:parent = "rootvariable" ; dicominfo:window_min = -34. ; dicominfo:window_max = 467.5 ; int dicom_groups ; dicom_groups:vartype = "group________" ; dicom_groups:varid = "MNI DICOM variable" ; dicom_groups:parent = "rootvariable" ; dicom_groups:children = "dicom_0x0008\n", "dicom_0x0010\n", "dicom_0x0018\n", "dicom_0x0019\n", "dicom_0x0020\n", "dicom_0x0021\n", "dicom_0x0023\n", "dicom_0x0028\n", "dicom_0x0029\n", "dicom_0x0032\n", "dicom_0x0040\n", "dicom_0x0051\n", "dicom_0x7fe0" ; int dicom_0x0008 ; dicom_0x0008:vartype = "group________" ; dicom_0x0008:varid = "MNI DICOM variable" ; dicom_0x0008:parent = "dicom_groups" ; dicom_0x0008:el_0x0000 = 0b, 0b, 3b, 112b ; dicom_0x0008:el_0x0005 = "ISO_IR 100" ; dicom_0x0008:el_0x0008 = "ORIGINAL\\PRIMARY\\M\\ND " ; dicom_0x0008:el_0x0016 = "1.2.840.10008.5.1.4.1.1.4" ; dicom_0x0008:el_0x0018 = "1.3.12.2.1107.5.2.14.16505.30000009032714261626500000429" ; dicom_0x0008:el_0x0020 = "20090327" ; dicom_0x0008:el_0x0021 = "20090327" ; dicom_0x0008:el_0x0022 = "20090327" ; dicom_0x0008:el_0x0023 = "20090327" ; dicom_0x0008:el_0x0030 = "101814.640000 " ; dicom_0x0008:el_0x0031 = "110250.203000 " ; dicom_0x0008:el_0x0032 = "104737.934998 " ; dicom_0x0008:el_0x0033 = "110252.171000 " ; dicom_0x0008:el_0x0050 = "" ; dicom_0x0008:el_0x0060 = "MR" ; dicom_0x0008:el_0x0070 = "SIEMENS " ; dicom_0x0008:el_0x0080 = "McConnell Brain Imaging Center" ; dicom_0x0008:el_0x0081 = "3801University, Montreal /5032D1/, Quebec, H3A2B4, CA " ; dicom_0x0008:el_0x0090 = "" ; dicom_0x0008:el_0x1010 = "MRC " ; dicom_0x0008:el_0x1030 = "FUNCTIONAL^Dr Lepage" ; dicom_0x0008:el_0x103e = "GLOBAL_no angulation" ; dicom_0x0008:el_0x1050 = "RESEARCH" ; dicom_0x0008:el_0x1070 = "lm" ; dicom_0x0008:el_0x1090 = "SonataVision" ; Colin Hawco, PhD Post Doctoral Researcher Temerty Centre for Therapeutic Brain Intervention Centre for Addiction and Mental Health (CAMH) University of Toronto "Disorder Expands" From colin.hawco at mail.mcgill.ca Wed Apr 3 12:40:37 2013 From: colin.hawco at mail.mcgill.ca (Colin Shaun Hawco, M) Date: Wed, 3 Apr 2013 16:40:37 +0000 Subject: [MINC-users] mincreeample transformation problem In-Reply-To: References: , Message-ID: And an example EPI Image netcdf epi_file { dimensions: zspace = 30 ; yspace = 64 ; xspace = 64 ; variables: int zspace ; zspace:varid = "MINC standard variable" ; zspace:vartype = "dimension____" ; zspace:version = "MINC Version 1.0" ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:step = 5.00000023980207 ; zspace:units = "mm" ; zspace:start = -69.2670692002613 ; zspace:direction_cosines = 0.0886361496853597, -0.0451411970661573, 0.995040655097262 ; int yspace ; yspace:varid = "MINC standard variable" ; yspace:vartype = "dimension____" ; yspace:version = "MINC Version 1.0" ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:step = 3.99999998616676 ; yspace:units = "mm" ; yspace:start = -114.419242845404 ; yspace:direction_cosines = -0.0666440429608072, 0.996465269196971, 0.0511423388402057 ; int xspace ; xspace:varid = "MINC standard variable" ; xspace:vartype = "dimension____" ; xspace:version = "MINC Version 1.0" ; xspace:comments = "X increases from patient left to right" ; xspace:spacing = "regular__" ; xspace:alignment = "centre" ; xspace:step = -3.9999998858578 ; xspace:units = "mm" ; xspace:start = 137.159234295035 ; xspace:direction_cosines = 0.993832080113542, 0.070846596891737, -0.0853144550826576 ; double image-max ; image-max:varid = "MINC standard variable" ; image-max:vartype = "var_attribute" ; image-max:version = "MINC Version 1.0" ; image-max:_FillValue = 1. ; image-max:parent = "image" ; double image-min ; image-min:varid = "MINC standard variable" ; image-min:vartype = "var_attribute" ; image-min:version = "MINC Version 1.0" ; image-min:_FillValue = 0. ; image-min:parent = "image" ; int study ; study:parent = "rootvariable" ; study:varid = "MINC standard variable" ; study:vartype = "group________" ; study:version = "MINC Version 1.0" ; int rootvariable ; rootvariable:varid = "MINC standard variable" ; rootvariable:vartype = "group________" ; rootvariable:version = "MINC Version 1.0" ; rootvariable:parent = "" ; rootvariable:children = "study\n", "patient\n", "acquisition\n", "image" ; int patient ; patient:parent = "rootvariable" ; patient:varid = "MINC standard variable" ; patient:vartype = "group________" ; patient:version = "MINC Version 1.0" ; patient:full_name = "3T 2D EP TR=3000ms/TE=30ms/FA=90deg 24-Jul-2012 11:33:1.78 Mosaic" ; int acquisition ; acquisition:parent = "rootvariable" ; acquisition:varid = "MINC standard variable" ; acquisition:vartype = "group________" ; acquisition:version = "MINC Version 1.0" ; short image(zspace, yspace, xspace) ; image:parent = "rootvariable" ; image:varid = "MINC standard variable" ; image:vartype = "group________" ; image:version = "MINC Version 1.0" ; image:image-max = "--->image-max" ; image:image-min = "--->image-min" ; image:signtype = "signed__" ; image:valid_range = 0., 2049. ; // global attributes: :ident = "chawc:node17:2013.03.05.09.52.34:17491:1" ; :minc_version = "2.1.01" ; :history = "Tue Mar 5 09:52:34 2013>>> nii2mnc -quiet tf240720121100-113301-00033-00033-1.hdr /imaging/scratch/Daskalakis/chawc/Data/minc/p121/run1/tf240720121100-113301-00033-00033-1.mnc\n", "" ; data: zspace = _ ; yspace = _ ; xspace = _ ; image-max = 2049 ; image-min = 0 ; study = _ ; rootvariable = _ ; patient = _ ; acquisition = _ ; } And just to be complete, the EPI Template image to which I want to resample the EPI data netcdf EPI_template { dimensions: zspace = 91 ; yspace = 109 ; xspace = 91 ; variables: int zspace ; zspace:varid = "MINC standard variable" ; zspace:vartype = "dimension____" ; zspace:version = "MINC Version 1.0" ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:step = 2. ; zspace:units = "mm" ; zspace:start = -72. ; zspace:direction_cosines = 0., 0., 1. ; int yspace ; yspace:varid = "MINC standard variable" ; yspace:vartype = "dimension____" ; yspace:version = "MINC Version 1.0" ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:step = 2. ; yspace:units = "mm" ; yspace:start = -126. ; yspace:direction_cosines = 0., 1., 0. ; int xspace ; xspace:varid = "MINC standard variable" ; xspace:vartype = "dimension____" ; xspace:version = "MINC Version 1.0" ; xspace:comments = "X increases from patient left to right" ; xspace:spacing = "regular__" ; xspace:alignment = "centre" ; xspace:step = -2. ; xspace:units = "mm" ; xspace:start = 90. ; xspace:direction_cosines = 1., -0., -0. ; double image-max ; image-max:varid = "MINC standard variable" ; image-max:vartype = "var_attribute" ; image-max:version = "MINC Version 1.0" ; image-max:_FillValue = 1. ; image-max:parent = "image" ; double image-min ; image-min:varid = "MINC standard variable" ; image-min:vartype = "var_attribute" ; image-min:version = "MINC Version 1.0" ; image-min:_FillValue = 0. ; image-min:parent = "image" ; int study ; study:parent = "rootvariable" ; study:varid = "MINC standard variable" ; study:vartype = "group________" ; study:version = "MINC Version 1.0" ; int rootvariable ; rootvariable:varid = "MINC standard variable" ; rootvariable:vartype = "group________" ; rootvariable:version = "MINC Version 1.0" ; rootvariable:parent = "" ; rootvariable:children = "study\n", "patient\n", "acquisition\n", "image" ; int patient ; patient:parent = "rootvariable" ; patient:varid = "MINC standard variable" ; patient:vartype = "group________" ; patient:version = "MINC Version 1.0" ; patient:full_name = "NIFTI-1 Image" ; int acquisition ; acquisition:parent = "rootvariable" ; acquisition:varid = "MINC standard variable" ; acquisition:vartype = "group________" ; acquisition:version = "MINC Version 1.0" ; byte image(zspace, yspace, xspace) ; image:parent = "rootvariable" ; image:varid = "MINC standard variable" ; image:vartype = "group________" ; image:version = "MINC Version 1.0" ; image:image-max = "--->image-max" ; image:image-min = "--->image-min" ; image:signtype = "unsigned" ; image:valid_range = 0., 255. ; // global attributes: :ident = "colin:penfield:2012.11.05.14.08.29:27799:1" ; :minc_version = "2.1.01" ; :history = "Mon Nov 5 14:08:29 2012>>> nii2mnc /projects/colin/work/spm8/templates/EPI.nii /projects/colin/EPI_template.mnc\n", "" ; data: zspace = _ ; yspace = _ ; xspace = _ ; image-max = 0.831372529501095 ; image-min = 0 ; study = _ ; rootvariable = _ ; patient = _ ; acquisition = _ ; } I very much appreciate the help! From a.janke at gmail.com Thu Apr 4 07:11:21 2013 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 4 Apr 2013 21:11:21 +1000 Subject: [MINC-users] mincreeample transformation problem In-Reply-To: References: Message-ID: Hi again Colin, On 4 April 2013 02:40, Colin Shaun Hawco, M wrote: > The attached file just showed an axial slice of EPI, with the data shirted forward such that the front of the brain is cut off by the edge of the image. > > Because of the size of the mincheaders, i need to split up the message. > > T1 image > > netcdf p121_anat { > dimensions: > xspace = 160 ; > zspace = 256 ; > yspace = 256 ; > variables: > double xspace(xspace) ; > xspace:varid = "MINC standard variable" ; > xspace:vartype = "dimension____" ; > xspace:version = "MINC Version 1.0" ; > xspace:comments = "X increases from patient left to right" ; > xspace:spacing = "regular__" ; > xspace:alignment = "centre" ; > xspace:step = 1. ; > xspace:start = -74.777108669281 ; > xspace:spacetype = "native____" ; > xspace:direction_cosines = 1., -0., 0. ; > int zspace ; > zspace:varid = "MINC standard variable" ; > zspace:vartype = "dimension____" ; > zspace:version = "MINC Version 1.0" ; > zspace:comments = "Z increases from patient inferior to superior" ; > zspace:spacing = "regular__" ; > zspace:alignment = "centre" ; > zspace:step = -1. ; > zspace:start = 125.30120491982 ; > zspace:spacetype = "native____" ; > zspace:direction_cosines = 0., 0., 1. ; Well from the above my guess was off, all the files do have regular spacing (look for regular__ above). So just to recap, the process for registration is as such: mincANTS T1.mnc -> MNI_model.mnc == T1-model.xfm mincANTS EPI.mnc -> T1.mnc == EPI-T1.xfm xfmconcat EPI-T1.xfm T1-model.xfm concat.xfm mincresample -like EPI_model.mnc -transformation concat.xfm EPI.mnc EPI_normalised.mnc ? And if you resample like the MNI_model things are good but if you resample like the EPI_model things go akimbo? a From colin.hawco at mail.mcgill.ca Wed Apr 3 12:38:41 2013 From: colin.hawco at mail.mcgill.ca (Colin Shaun Hawco, M) Date: Wed, 3 Apr 2013 16:38:41 +0000 Subject: [MINC-users] mincreeample transformation problem Message-ID: Thanks for the replies, The attached file just showed an axial slice of EPI, with the data shirted forward such that the front of the brain is cut off by the edge of the image. OK, here are the mincheaders (this will be a bit of a long message): T1 image netcdf p121_anat { dimensions: xspace = 160 ; zspace = 256 ; yspace = 256 ; variables: double xspace(xspace) ; xspace:varid = "MINC standard variable" ; xspace:vartype = "dimension____" ; xspace:version = "MINC Version 1.0" ; xspace:comments = "X increases from patient left to right" ; xspace:spacing = "regular__" ; xspace:alignment = "centre" ; xspace:step = 1. ; xspace:start = -74.777108669281 ; xspace:spacetype = "native____" ; xspace:direction_cosines = 1., -0., 0. ; int zspace ; zspace:varid = "MINC standard variable" ; zspace:vartype = "dimension____" ; zspace:version = "MINC Version 1.0" ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:step = -1. ; zspace:start = 125.30120491982 ; zspace:spacetype = "native____" ; zspace:direction_cosines = 0., 0., 1. ; int yspace ; yspace:varid = "MINC standard variable" ; yspace:vartype = "dimension____" ; yspace:version = "MINC Version 1.0" ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:step = -1. ; yspace:start = 167.1325302124 ; yspace:spacetype = "native____" ; yspace:direction_cosines = 0., 1., -0. ; short image(xspace, zspace, yspace) ; image:parent = "rootvariable" ; image:varid = "MINC standard variable" ; image:vartype = "group________" ; image:version = "MINC Version 1.0" ; image:signtype = "signed__" ; image:valid_range = 0., 4095. ; image:complete = "true_" ; image:image-min = "--->image-min" ; image:image-max = "--->image-max" ; int rootvariable ; rootvariable:varid = "MINC standard variable" ; rootvariable:vartype = "group________" ; rootvariable:version = "MINC Version 1.0" ; rootvariable:parent = "" ; rootvariable:children = "image\n", "patient\n", "study\n", "acquisition\n", "dicominfo\n", "dicom_groups" ; double image-min(xspace) ; image-min:varid = "MINC standard variable" ; image-min:vartype = "var_attribute" ; image-min:version = "MINC Version 1.0" ; image-min:_FillValue = 0. ; image-min:parent = "image" ; double image-max(xspace) ; image-max:varid = "MINC standard variable" ; image-max:vartype = "var_attribute" ; image-max:version = "MINC Version 1.0" ; image-max:_FillValue = 1. ; image-max:parent = "image" ; int patient ; patient:parent = "rootvariable" ; patient:varid = "MINC standard variable" ; patient:vartype = "group________" ; patient:version = "MINC Version 1.0" ; patient:full_name = "pt121" ; patient:identification = "09.03.27-10:18:12-DST-1.3.12.2.1107.5.2.14.16505" ; patient:birthdate = "19830703" ; patient:age = "025Y" ; patient:sex = "female" ; patient:weight = 57. ; int study ; study:parent = "rootvariable" ; study:varid = "MINC standard variable" ; study:vartype = "group________" ; study:version = "MINC Version 1.0" ; study:start_date = "20090327" ; study:start_time = "101814.640000 " ; study:modality = "MRI__" ; study:manufacturer = "SIEMENS " ; study:model = "SonataVision" ; study:field_value = 1.5 ; study:software_version = "syngo MR A30 4VA30A " ; study:serial_no = "16505 " ; study:calibration_date = "20050630" ; study:institution = "McConnell Brain Imaging Center" ; study:station_id = "MRC " ; study:performing_physician = "" ; study:operator = "lm" ; study:procedure = "FUNCTIONAL^Dr Lepage" ; study:study_id = "20090328.101814" ; int acquisition ; acquisition:parent = "rootvariable" ; acquisition:varid = "MINC standard variable" ; acquisition:vartype = "group________" ; acquisition:version = "MINC Version 1.0" ; acquisition:acquisition_id = "4" ; acquisition:start_time = "20090327 101814.640000 " ; acquisition:scanning_sequence = "*fl3d1_ns " ; acquisition:protocol_name = "GLOBAL_no angulation" ; acquisition:receive_coil = "CP_HeadArray" ; acquisition:transmit_coil = "Body" ; acquisition:repetition_time = 0.022 ; acquisition:echo_time = 0.0092 ; acquisition:echo_number = 0. ; acquisition:flip_angle = 30. ; acquisition:slice_thickness = 1. ; acquisition:num_slices = 1. ; acquisition:num_dyn_scans = 1. ; acquisition:num_averages = 1. ; acquisition:imaging_frequency = 63687939. ; acquisition:imaged_nucleus = "1H" ; acquisition:window_center = 46. ; acquisition:window_width = 135. ; acquisition:num_phase_enc_steps = 256. ; acquisition:percent_sampling = 10000. ; acquisition:percent_phase_fov = 10000. ; acquisition:pixel_bandwidth = 70. ; acquisition:phase_enc_dir = "ROW" ; acquisition:SAR = 0.03627666831017 ; acquisition:mr_acq_type = "3D" ; acquisition:image_type = "ORIGINAL\\PRIMARY\\M\\ND " ; acquisition:MrProt_dump = "disabled" ; int dicominfo ; dicominfo:vartype = "group________" ; dicominfo:varid = "MNI DICOM information variable" ; dicominfo:parent = "rootvariable" ; dicominfo:window_min = -34. ; dicominfo:window_max = 467.5 ; int dicom_groups ; dicom_groups:vartype = "group________" ; dicom_groups:varid = "MNI DICOM variable" ; dicom_groups:parent = "rootvariable" ; dicom_groups:children = "dicom_0x0008\n", "dicom_0x0010\n", "dicom_0x0018\n", "dicom_0x0019\n", "dicom_0x0020\n", "dicom_0x0021\n", "dicom_0x0023\n", "dicom_0x0028\n", "dicom_0x0029\n", "dicom_0x0032\n", "dicom_0x0040\n", "dicom_0x0051\n", "dicom_0x7fe0" ; int dicom_0x0008 ; dicom_0x0008:vartype = "group________" ; dicom_0x0008:varid = "MNI DICOM variable" ; dicom_0x0008:parent = "dicom_groups" ; dicom_0x0008:el_0x0000 = 0b, 0b, 3b, 112b ; dicom_0x0008:el_0x0005 = "ISO_IR 100" ; dicom_0x0008:el_0x0008 = "ORIGINAL\\PRIMARY\\M\\ND " ; dicom_0x0008:el_0x0016 = "1.2.840.10008.5.1.4.1.1.4" ; dicom_0x0008:el_0x0018 = "1.3.12.2.1107.5.2.14.16505.30000009032714261626500000429" ; dicom_0x0008:el_0x0020 = "20090327" ; dicom_0x0008:el_0x0021 = "20090327" ; dicom_0x0008:el_0x0022 = "20090327" ; dicom_0x0008:el_0x0023 = "20090327" ; dicom_0x0008:el_0x0030 = "101814.640000 " ; dicom_0x0008:el_0x0031 = "110250.203000 " ; dicom_0x0008:el_0x0032 = "104737.934998 " ; dicom_0x0008:el_0x0033 = "110252.171000 " ; dicom_0x0008:el_0x0050 = "" ; dicom_0x0008:el_0x0060 = "MR" ; dicom_0x0008:el_0x0070 = "SIEMENS " ; dicom_0x0008:el_0x0080 = "McConnell Brain Imaging Center" ; dicom_0x0008:el_0x0081 = "3801University, Montreal /5032D1/, Quebec, H3A2B4, CA " ; dicom_0x0008:el_0x0090 = "" ; dicom_0x0008:el_0x1010 = "MRC " ; dicom_0x0008:el_0x1030 = "FUNCTIONAL^Dr Lepage" ; dicom_0x0008:el_0x103e = "GLOBAL_no angulation" ; dicom_0x0008:el_0x1050 = "RESEARCH" ; dicom_0x0008:el_0x1070 = "lm" ; dicom_0x0008:el_0x1090 = "SonataVision" ; And an example EPI Image netcdf epi_file { dimensions: zspace = 30 ; yspace = 64 ; xspace = 64 ; variables: int zspace ; zspace:varid = "MINC standard variable" ; zspace:vartype = "dimension____" ; zspace:version = "MINC Version 1.0" ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:step = 5.00000023980207 ; zspace:units = "mm" ; zspace:start = -69.2670692002613 ; zspace:direction_cosines = 0.0886361496853597, -0.0451411970661573, 0.995040655097262 ; int yspace ; yspace:varid = "MINC standard variable" ; yspace:vartype = "dimension____" ; yspace:version = "MINC Version 1.0" ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:step = 3.99999998616676 ; yspace:units = "mm" ; yspace:start = -114.419242845404 ; yspace:direction_cosines = -0.0666440429608072, 0.996465269196971, 0.0511423388402057 ; int xspace ; xspace:varid = "MINC standard variable" ; xspace:vartype = "dimension____" ; xspace:version = "MINC Version 1.0" ; xspace:comments = "X increases from patient left to right" ; xspace:spacing = "regular__" ; xspace:alignment = "centre" ; xspace:step = -3.9999998858578 ; xspace:units = "mm" ; xspace:start = 137.159234295035 ; xspace:direction_cosines = 0.993832080113542, 0.070846596891737, -0.0853144550826576 ; double image-max ; image-max:varid = "MINC standard variable" ; image-max:vartype = "var_attribute" ; image-max:version = "MINC Version 1.0" ; image-max:_FillValue = 1. ; image-max:parent = "image" ; double image-min ; image-min:varid = "MINC standard variable" ; image-min:vartype = "var_attribute" ; image-min:version = "MINC Version 1.0" ; image-min:_FillValue = 0. ; image-min:parent = "image" ; int study ; study:parent = "rootvariable" ; study:varid = "MINC standard variable" ; study:vartype = "group________" ; study:version = "MINC Version 1.0" ; int rootvariable ; rootvariable:varid = "MINC standard variable" ; rootvariable:vartype = "group________" ; rootvariable:version = "MINC Version 1.0" ; rootvariable:parent = "" ; rootvariable:children = "study\n", "patient\n", "acquisition\n", "image" ; int patient ; patient:parent = "rootvariable" ; patient:varid = "MINC standard variable" ; patient:vartype = "group________" ; patient:version = "MINC Version 1.0" ; patient:full_name = "3T 2D EP TR=3000ms/TE=30ms/FA=90deg 24-Jul-2012 11:33:1.78 Mosaic" ; int acquisition ; acquisition:parent = "rootvariable" ; acquisition:varid = "MINC standard variable" ; acquisition:vartype = "group________" ; acquisition:version = "MINC Version 1.0" ; short image(zspace, yspace, xspace) ; image:parent = "rootvariable" ; image:varid = "MINC standard variable" ; image:vartype = "group________" ; image:version = "MINC Version 1.0" ; image:image-max = "--->image-max" ; image:image-min = "--->image-min" ; image:signtype = "signed__" ; image:valid_range = 0., 2049. ; // global attributes: :ident = "chawc:node17:2013.03.05.09.52.34:17491:1" ; :minc_version = "2.1.01" ; :history = "Tue Mar 5 09:52:34 2013>>> nii2mnc -quiet tf240720121100-113301-00033-00033-1.hdr /imaging/scratch/Daskalakis/chawc/Data/minc/p121/run1/tf240720121100-113301-00033-00033-1.mnc\n", "" ; data: zspace = _ ; yspace = _ ; xspace = _ ; image-max = 2049 ; image-min = 0 ; study = _ ; rootvariable = _ ; patient = _ ; acquisition = _ ; } And just to be complete, the EPI Template image to which I want to resample the EPI data netcdf EPI_template { dimensions: zspace = 91 ; yspace = 109 ; xspace = 91 ; variables: int zspace ; zspace:varid = "MINC standard variable" ; zspace:vartype = "dimension____" ; zspace:version = "MINC Version 1.0" ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:step = 2. ; zspace:units = "mm" ; zspace:start = -72. ; zspace:direction_cosines = 0., 0., 1. ; int yspace ; yspace:varid = "MINC standard variable" ; yspace:vartype = "dimension____" ; yspace:version = "MINC Version 1.0" ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:step = 2. ; yspace:units = "mm" ; yspace:start = -126. ; yspace:direction_cosines = 0., 1., 0. ; int xspace ; xspace:varid = "MINC standard variable" ; xspace:vartype = "dimension____" ; xspace:version = "MINC Version 1.0" ; xspace:comments = "X increases from patient left to right" ; xspace:spacing = "regular__" ; xspace:alignment = "centre" ; xspace:step = -2. ; xspace:units = "mm" ; xspace:start = 90. ; xspace:direction_cosines = 1., -0., -0. ; double image-max ; image-max:varid = "MINC standard variable" ; image-max:vartype = "var_attribute" ; image-max:version = "MINC Version 1.0" ; image-max:_FillValue = 1. ; image-max:parent = "image" ; double image-min ; image-min:varid = "MINC standard variable" ; image-min:vartype = "var_attribute" ; image-min:version = "MINC Version 1.0" ; image-min:_FillValue = 0. ; image-min:parent = "image" ; int study ; study:parent = "rootvariable" ; study:varid = "MINC standard variable" ; study:vartype = "group________" ; study:version = "MINC Version 1.0" ; int rootvariable ; rootvariable:varid = "MINC standard variable" ; rootvariable:vartype = "group________" ; rootvariable:version = "MINC Version 1.0" ; rootvariable:parent = "" ; rootvariable:children = "study\n", "patient\n", "acquisition\n", "image" ; int patient ; patient:parent = "rootvariable" ; patient:varid = "MINC standard variable" ; patient:vartype = "group________" ; patient:version = "MINC Version 1.0" ; patient:full_name = "NIFTI-1 Image" ; int acquisition ; acquisition:parent = "rootvariable" ; acquisition:varid = "MINC standard variable" ; acquisition:vartype = "group________" ; acquisition:version = "MINC Version 1.0" ; byte image(zspace, yspace, xspace) ; image:parent = "rootvariable" ; image:varid = "MINC standard variable" ; image:vartype = "group________" ; image:version = "MINC Version 1.0" ; image:image-max = "--->image-max" ; image:image-min = "--->image-min" ; image:signtype = "unsigned" ; image:valid_range = 0., 255. ; // global attributes: :ident = "colin:penfield:2012.11.05.14.08.29:27799:1" ; :minc_version = "2.1.01" ; :history = "Mon Nov 5 14:08:29 2012>>> nii2mnc /projects/colin/work/spm8/templates/EPI.nii /projects/colin/EPI_template.mnc\n", "" ; data: zspace = _ ; yspace = _ ; xspace = _ ; image-max = 0.831372529501095 ; image-min = 0 ; study = _ ; rootvariable = _ ; patient = _ ; acquisition = _ ; } I very much appreciate the help! Colin Hawco, PhD Post Doctoral Researcher Temerty Centre for Therapeutic Brain Intervention Centre for Addiction and Mental Health (CAMH) University of Toronto "Disorder Expands" From colin.hawco at mail.mcgill.ca Thu Apr 4 12:08:41 2013 From: colin.hawco at mail.mcgill.ca (Colin Shaun Hawco, M) Date: Thu, 4 Apr 2013 16:08:41 +0000 Subject: [MINC-users] mincreeample transformation problem In-Reply-To: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> Message-ID: That is almost the steps I am doing, only for the transform for EPI to T1, i am using mritoself, with a linear transform (which works on all other data sets except this one). Also, for resampling, things work if I resample using -like the original EPI file (which then should not change the file dimentions or start points). So this command gives a reasonable (but not useable on a practical level) output: mincresample -like epi_file.mnc -transform concat.xfm epi_file.mnc epi_normalized.mnc However, if I use -like EPI_model.mnc, the registration fails, and the data is shifted partially out of range. But in order to perform my group analysis, I need the EPI data in the space, with the dimensions and start points, of the EPI_model. I have the feeling there is a problem with translating/moving the origon, but I lack the sophistication in minctools to figure out how. Well from the above my guess was off, all the files do have regular spacing (look for regular__ above). So just to recap, the process for registration is as such: mincANTS T1.mnc -> MNI_model.mnc == T1-model.xfm mincANTS EPI.mnc -> T1.mnc == EPI-T1.xfm xfmconcat EPI-T1.xfm T1-model.xfm concat.xfm mincresample -like EPI_model.mnc -transformation concat.xfm EPI.mnc EPI_normalised.mnc ? And if you resample like the MNI_model things are good but if you resample like the EPI_model things go akimbo? a From vladimir.fonov at gmail.com Thu Apr 4 13:23:42 2013 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 04 Apr 2013 13:23:42 -0400 Subject: [MINC-users] mincreeample transformation problem In-Reply-To: References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> Message-ID: <515DB71E.8010905@gmail.com> Hello, On 13-04-04 12:08 PM, Colin Shaun Hawco, M wrote: > So just to recap, the process for registration is as such: > > mincANTS T1.mnc -> MNI_model.mnc == T1-model.xfm > > mincANTS EPI.mnc -> T1.mnc == EPI-T1.xfm > > xfmconcat EPI-T1.xfm T1-model.xfm concat.xfm > > mincresample -like EPI_model.mnc -transformation concat.xfm EPI.mnc > EPI_normalised.mnc > > ? > > And if you resample like the MNI_model things are good but if you > resample like the EPI_model things go akimbo? So, isn't it what's intended : T1-model.xfm -maps from T1.mnc to MNI_model and EPI-T1.xfm -maps from EPI to T1.mnc so, concat.xfm - maps from EPI to MNI_model how do you coregister EPI_model and MNI_model ? -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From colin.hawco at mail.mcgill.ca Thu Apr 4 13:40:17 2013 From: colin.hawco at mail.mcgill.ca (Colin Shaun Hawco, M) Date: Thu, 4 Apr 2013 17:40:17 +0000 Subject: [MINC-users] mincreeample transformation problem In-Reply-To: <515DB71E.8010905@gmail.com> References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> , <515DB71E.8010905@gmail.com> Message-ID: The EPI model is already in MNI space. It is the EPI template from SPM8. It is perfectly coregistered with the MNI152 template. in fact, the only reason for using the EPI_model at all is to move the data into a common space (in terms of voxel size and dimensions) for group comparison, and to make it possible for me to compare activities across studies. It occurs to me one possible solution to my problem is to abandon this step of resampling into the EPI model space. I am doing it as a sort of carry over from the way SPM does the normalization. But it is interpolating the data and resampling my voxels to 2x2x2 mm. I am not sure I see any good reason to do so, and maybe the best approach would be to keep the data in the native voxel size. Colin Hawco, PhD Post Doctoral Researcher Temerty Centre for Therapeutic Brain Intervention Centre for Addiction and Mental Health (CAMH) University of Toronto "Disorder Expands" ________________________________________ From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of Vladimir S. FONOV [vladimir.fonov at gmail.com] Sent: Thursday, April 04, 2013 1:23 PM To: minc-users at bic.mni.mcgill.ca Subject: Re: [MINC-users] mincreeample transformation problem Hello, On 13-04-04 12:08 PM, Colin Shaun Hawco, M wrote: > So just to recap, the process for registration is as such: > > mincANTS T1.mnc -> MNI_model.mnc == T1-model.xfm > > mincANTS EPI.mnc -> T1.mnc == EPI-T1.xfm > > xfmconcat EPI-T1.xfm T1-model.xfm concat.xfm > > mincresample -like EPI_model.mnc -transformation concat.xfm EPI.mnc > EPI_normalised.mnc > > ? > > And if you resample like the MNI_model things are good but if you > resample like the EPI_model things go akimbo? So, isn't it what's intended : T1-model.xfm -maps from T1.mnc to MNI_model and EPI-T1.xfm -maps from EPI to T1.mnc so, concat.xfm - maps from EPI to MNI_model how do you coregister EPI_model and MNI_model ? -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Thu Apr 4 19:42:47 2013 From: a.janke at gmail.com (Andrew Janke) Date: Fri, 5 Apr 2013 09:42:47 +1000 Subject: [MINC-users] mincreeample transformation problem In-Reply-To: References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> Message-ID: On 5 April 2013 02:08, Colin Shaun Hawco, M wrote: > That is almost the steps I am doing, only for the transform for EPI to T1, i am using mritoself, with a linear transform (which works on all other data sets except this one). > > Also, for resampling, things work if I resample using -like the original EPI file (which then should not change the file dimentions or start points). So this command gives a reasonable (but not useable on a practical level) output: > > mincresample -like epi_file.mnc -transform concat.xfm epi_file.mnc epi_normalized.mnc Can you please explain what you mean by "things work" here? If you load epi_normalized.mnc and your EPI_model in register they are aligned or are you just meaning that the resulting file is still "all there"? > However, if I use -like EPI_model.mnc, the registration fails, and the data is shifted partially out of range. But in order to perform my group analysis, I need the EPI data in the space, with the dimensions and start points, of the EPI_model. There should be no problem getting this to happen but I am now starting to suspect that your EPI->T1 registration is off. > I have the feeling there is a problem with translating/moving the origon, but I lack the sophistication in minctools to figure out how. Origin location should not come into it. minctracc/mincANTS outputs a transformation matrix that is unaffected by such things. a From colin.hawco at mail.mcgill.ca Mon Apr 8 16:01:33 2013 From: colin.hawco at mail.mcgill.ca (Colin Shaun Hawco, M) Date: Mon, 8 Apr 2013 20:01:33 +0000 Subject: [MINC-users] mincreeample transformation problem In-Reply-To: References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> , Message-ID: Thanks for the reply, and sorry for my late return. Andrew, I think you were right, the problem was in my EPI > T1. I recalculated the transform, and reran the whole routine, and this time I was able to get it to work nicely. So the problem appears to be solved. Thanks a lot to everyone for their help. : ) Colin Hawco, PhD Post Doctoral Researcher Temerty Centre for Therapeutic Brain Intervention Centre for Addiction and Mental Health (CAMH) University of Toronto "Disorder Expands" ________________________________________ From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of Andrew Janke [a.janke at gmail.com] Sent: Thursday, April 04, 2013 7:42 PM To: MINC users mailing list Subject: Re: [MINC-users] mincreeample transformation problem On 5 April 2013 02:08, Colin Shaun Hawco, M wrote: > That is almost the steps I am doing, only for the transform for EPI to T1, i am using mritoself, with a linear transform (which works on all other data sets except this one). > > Also, for resampling, things work if I resample using -like the original EPI file (which then should not change the file dimentions or start points). So this command gives a reasonable (but not useable on a practical level) output: > > mincresample -like epi_file.mnc -transform concat.xfm epi_file.mnc epi_normalized.mnc Can you please explain what you mean by "things work" here? If you load epi_normalized.mnc and your EPI_model in register they are aligned or are you just meaning that the resulting file is still "all there"? > However, if I use -like EPI_model.mnc, the registration fails, and the data is shifted partially out of range. But in order to perform my group analysis, I need the EPI data in the space, with the dimensions and start points, of the EPI_model. There should be no problem getting this to happen but I am now starting to suspect that your EPI->T1 registration is off. > I have the feeling there is a problem with translating/moving the origon, but I lack the sophistication in minctools to figure out how. Origin location should not come into it. minctracc/mincANTS outputs a transformation matrix that is unaffected by such things. a _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From pgravel at bic.mni.mcgill.ca Mon Apr 8 17:53:33 2013 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Mon, 8 Apr 2013 17:53:33 -0400 (EDT) Subject: [MINC-users] upet2mnc problem In-Reply-To: References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> , Message-ID: Dear All, Quick question: I would like to convert microPET images (scanned on our Concorde microPET R4 at the MNI) to MINC format using upet2mnc, but I get the following error: ================================================================================= /usr/local/bic/bin/upet2mnc A1441_12-03-13_v3_39frameFBP.img A1441_12-03-13_v3_39frameFBP.mnc Starting conversion - Input header: A1441_12-03-13_v3_39frameFBP.img.hdr - Input image: A1441_12-03-13_v3_39frameFBP.img - Output file: A1441_12-03-13_v3_39frameFBP.mnc WARNING: Unrecognized keyword manufacturer Segmentation fault ================================================================================= I also tried the version under /usr/local/mni/bin/ but to no avail. Before looking into wrting another script/binary to do this (yes, I'm being lazy ;-)!), would anyone have any idea as to what caused this error? Many thanks! Paul From vladimir.fonov at gmail.com Mon Apr 8 17:58:46 2013 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Mon, 8 Apr 2013 17:58:46 -0400 Subject: [MINC-users] upet2mnc problem In-Reply-To: References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> Message-ID: Hello, I remember that some upet2mnc programs had a bug which manifested itself when program was compiled on 64bit - could it be your case (i.e try using 32bit binary)? On Mon, Apr 8, 2013 at 5:53 PM, Paul GRAVEL wrote: > Dear All, > > Quick question: > > I would like to convert microPET images (scanned on our Concorde microPET R4 > at the MNI) to MINC format using upet2mnc, but I get the following error: > ================================================================================= > /usr/local/bic/bin/upet2mnc A1441_12-03-13_v3_39frameFBP.img > A1441_12-03-13_v3_39frameFBP.mnc > Starting conversion > - Input header: A1441_12-03-13_v3_39frameFBP.img.hdr > - Input image: A1441_12-03-13_v3_39frameFBP.img > - Output file: A1441_12-03-13_v3_39frameFBP.mnc > WARNING: Unrecognized keyword manufacturer > Segmentation fault > ================================================================================= > > I also tried the version under /usr/local/mni/bin/ but to no avail. > > Before looking into wrting another script/binary to do this (yes, I'm being > lazy ;-)!), would anyone have any idea as to what caused this error? > > Many thanks! > > Paul > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- Best regards, Vladimir S. Fonov ~ vladimir fonov gmail com From pgravel at bic.mni.mcgill.ca Mon Apr 8 18:27:01 2013 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Mon, 8 Apr 2013 18:27:01 -0400 (EDT) Subject: [MINC-users] upet2mnc problem In-Reply-To: References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> Message-ID: Thanks Valdimir! I ran /usr/local/bic/bin/upet2mnc on 'agrippa' ( Debian GNU/Linux 6.0.7 (squeeze) ) and it does work fine; I originally ran the binary on Debian GNU/Linux 5.0.10 (lenny), where it crashed. Is this a Linux 'flavor' related problem...? Best Regards, Paul On Mon, 8 Apr 2013, Vladimir S. FONOV wrote: > Hello, > > I remember that some upet2mnc programs had a bug which manifested > itself when program was compiled on 64bit - could it be your case (i.e > try using 32bit binary)? > > On Mon, Apr 8, 2013 at 5:53 PM, Paul GRAVEL wrote: >> Dear All, >> >> Quick question: >> >> I would like to convert microPET images (scanned on our Concorde microPET R4 >> at the MNI) to MINC format using upet2mnc, but I get the following error: >> ================================================================================= >> /usr/local/bic/bin/upet2mnc A1441_12-03-13_v3_39frameFBP.img >> A1441_12-03-13_v3_39frameFBP.mnc >> Starting conversion >> - Input header: A1441_12-03-13_v3_39frameFBP.img.hdr >> - Input image: A1441_12-03-13_v3_39frameFBP.img >> - Output file: A1441_12-03-13_v3_39frameFBP.mnc >> WARNING: Unrecognized keyword manufacturer >> Segmentation fault >> ================================================================================= >> >> I also tried the version under /usr/local/mni/bin/ but to no avail. >> >> Before looking into wrting another script/binary to do this (yes, I'm being >> lazy ;-)!), would anyone have any idea as to what caused this error? >> >> Many thanks! >> >> Paul >> >> >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > -- > Best regards, > > Vladimir S. Fonov ~ vladimir fonov gmail com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Mon Apr 8 18:33:00 2013 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 9 Apr 2013 08:33:00 +1000 Subject: [MINC-users] upet2mnc problem In-Reply-To: References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> Message-ID: I had thought this was fixed at least in the version on github? https://github.com/BIC-MNI/minc-tools/blob/master/conversion/micropet/upet2mnc.c Mind you the error you are seeing "WARNING: Unrecognized keyword manufacturer" would insinuate that upet2mnc needs to know about the particular flavour of uPET data that your machine is producing. a On 9 April 2013 07:58, Vladimir S. FONOV wrote: > Hello, > > I remember that some upet2mnc programs had a bug which manifested > itself when program was compiled on 64bit - could it be your case (i.e > try using 32bit binary)? > > On Mon, Apr 8, 2013 at 5:53 PM, Paul GRAVEL wrote: >> Dear All, >> >> Quick question: >> >> I would like to convert microPET images (scanned on our Concorde microPET R4 >> at the MNI) to MINC format using upet2mnc, but I get the following error: >> ================================================================================= >> /usr/local/bic/bin/upet2mnc A1441_12-03-13_v3_39frameFBP.img >> A1441_12-03-13_v3_39frameFBP.mnc >> Starting conversion >> - Input header: A1441_12-03-13_v3_39frameFBP.img.hdr >> - Input image: A1441_12-03-13_v3_39frameFBP.img >> - Output file: A1441_12-03-13_v3_39frameFBP.mnc >> WARNING: Unrecognized keyword manufacturer >> Segmentation fault >> ================================================================================= >> >> I also tried the version under /usr/local/mni/bin/ but to no avail. >> >> Before looking into wrting another script/binary to do this (yes, I'm being >> lazy ;-)!), would anyone have any idea as to what caused this error? >> >> Many thanks! >> >> Paul >> >> >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > -- > Best regards, > > Vladimir S. Fonov ~ vladimir fonov gmail com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From a.janke at gmail.com Mon Apr 8 18:34:26 2013 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 9 Apr 2013 08:34:26 +1000 Subject: [MINC-users] upet2mnc problem In-Reply-To: References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> Message-ID: Well then I'd say Vladimir is on the mark. You can run dpkg --print-architecture on both machines if Debian/Ubuntu to find out which is 32 bit and which is 64. "lsb_release -a" might also be informative. a On 9 April 2013 08:27, Paul GRAVEL wrote: > I ran /usr/local/bic/bin/upet2mnc on 'agrippa' ( Debian GNU/Linux 6.0.7 > (squeeze) ) and it does work fine; I originally ran the binary on Debian > GNU/Linux 5.0.10 (lenny), where it crashed. Is this a Linux 'flavor' related > problem...? From pgravel at bic.mni.mcgill.ca Mon Apr 8 18:57:57 2013 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Mon, 8 Apr 2013 18:57:57 -0400 (EDT) Subject: [MINC-users] upet2mnc problem In-Reply-To: References: <841_1365084278_515D8876_841_80_1_BAD04089361149478D06D37F43F67D34107C0F51@EXMBX2010-5.campus.MCGILL.CA> Message-ID: Thanks Andrew! I ran "dpkg --print-architecture" and I get: amd64 on both machines. I had run "lsb_release -a" as well and I obtained: 1) On 'vaux' (the original machine that returned the error: No LSB modules are available. Distributor ID: Debian Description: Debian GNU/Linux 5.0.10 (lenny) Release: 5.0.10 Codename: lenny 2) on 'agrippa' (the machine on which the upet2mnc located under /usr/local/bic/bin/ works fine): No LSB modules are available. Distributor ID: Debian Description: Debian GNU/Linux 6.0.7 (squeeze) Release: 6.0.7 Codename: squeeze So both machines are 64bits. Hence my comment about the Linux flavor... But looking at "ldd /usr/local/bic/bin/upet2mnc" returns different outputs: 1) On vaux: linux-vdso.so.1 => (0x00007fffbe0b3000) libz.so.1 => /usr/lib/libz.so.1 (0x00007fb6a7339000) libm.so.6 => /lib/libm.so.6 (0x00007fb6a70b6000) libc.so.6 => /lib/libc.so.6 (0x00007fb6a6d63000) /lib64/ld-linux-x86-64.so.2 (0x00007fb6a7550000) 2) on agrippa: linux-vdso.so.1 => (0x00007fff51dff000) librt.so.1 => /lib/librt.so.1 (0x00007f9f23b91000) libz.so.1 => /usr/lib/libz.so.1 (0x00007f9f2397a000) libm.so.6 => /lib/libm.so.6 (0x00007f9f236f7000) libc.so.6 => /lib/libc.so.6 (0x00007f9f23395000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f9f23179000) /lib64/ld-linux-x86-64.so.2 (0x00007f9f23db3000) So, as a workaround I copied /usr/local/bic/bin/upet2mnc from 'agrippa' to 'vaux' and it does work fine. At some point I may look into recompling upet2mnc.c on 'vaux', but for now I am happy with this. Many thanks! Paul On Tue, 9 Apr 2013, Andrew Janke wrote: > Well then I'd say Vladimir is on the mark. > > You can run > > dpkg --print-architecture > > on both machines if Debian/Ubuntu to find out which is 32 bit and > which is 64. "lsb_release -a" might also be informative. > > > a > > > On 9 April 2013 08:27, Paul GRAVEL wrote: >> I ran /usr/local/bic/bin/upet2mnc on 'agrippa' ( Debian GNU/Linux 6.0.7 >> (squeeze) ) and it does work fine; I originally ran the binary on Debian >> GNU/Linux 5.0.10 (lenny), where it crashed. Is this a Linux 'flavor' related >> problem...? > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From a.janke at gmail.com Mon Apr 8 22:06:17 2013 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 9 Apr 2013 12:06:17 +1000 Subject: [MINC-users] Automated WM hyperintensity Message-ID: Hi all, I have a few things I use to identify WM hyperintensities predominately based upon classify with a few priors and manually segmented examples but am wondering if others out there have something unsupervised for this? thanks a From jonathan.m.dubois at gmail.com Sat Apr 13 17:17:13 2013 From: jonathan.m.dubois at gmail.com (Jonathan DuBois) Date: Sat, 13 Apr 2013 17:17:13 -0400 Subject: [MINC-users] Trouble installing RMINC Message-ID: Hi Minc Users, I am having some trouble installing RMINC on my Mac. I followed the direction here: https://github.com/mcvaneede/RMINC. The specific commands and errors are below. Any help would be appreciated. Alternatively, is there a minc function to export the values and coordinates of a minc file to a csv or text file that could imported into R, manipulated, and written back to a minc file? ###################### :/usr/local$ export R_LIBS=/usr/local/ :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC :/usr/local$ cd RMINC :/usr/local/RMINC$ ./autogen.sh ./autogen.sh: line 1: aclocal: command not found ./autogen.sh: line 2: autoconf: command not found :/usr/local/RMINC$ cd .. :/usr/local$ sudo R CMD INSTALL RMINC /Library/Frameworks/R.framework/Versions/3.0/Resources/library --configure-args='--with-build-path=/usr/local/bic' Warning: invalid package ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? * installing to library ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? * installing *source* package ?RMINC? ... ERROR: a 'NAMESPACE' file is required * removing ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC? ###################### Thanks Jon DuBois From vladimir.fonov at gmail.com Sat Apr 13 17:21:02 2013 From: vladimir.fonov at gmail.com (Vladimir S. Fonov) Date: Sat, 13 Apr 2013 17:21:02 -0400 Subject: [MINC-users] Trouble installing RMINC In-Reply-To: References: Message-ID: <5169CC3E.50207@gmail.com> Hello, looks like you don't have autoconf/automake installed on your system - > ./autogen.sh: line 1: aclocal: command not found > ./autogen.sh: line 2: autoconf: command not found indicates that these commands are missing On 13-04-13 05:17 PM, Jonathan DuBois wrote: > Hi Minc Users, > > I am having some trouble installing RMINC on my Mac. I followed the > direction here: https://github.com/mcvaneede/RMINC. The specific commands > and errors are below. Any help would be appreciated. > > Alternatively, is there a minc function to export the values and > coordinates of a minc file to a csv or text file that could imported into > R, manipulated, and written back to a minc file? > > ###################### > :/usr/local$ export R_LIBS=/usr/local/ > :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC > :/usr/local$ cd RMINC > :/usr/local/RMINC$ ./autogen.sh > ./autogen.sh: line 1: aclocal: command not found > ./autogen.sh: line 2: autoconf: command not found > :/usr/local/RMINC$ cd .. > :/usr/local$ sudo R CMD INSTALL RMINC > /Library/Frameworks/R.framework/Versions/3.0/Resources/library > --configure-args='--with-build-path=/usr/local/bic' > Warning: invalid package > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > * installing to library > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > * installing *source* package ?RMINC? ... > ERROR: a 'NAMESPACE' file is required > * removing > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC? -- Best regards, Vladimir S. Fonov ~ vladimir.fonov gmail.com From jason at phenogenomics.ca Sat Apr 13 17:24:47 2013 From: jason at phenogenomics.ca (Jason Lerch) Date: Sat, 13 Apr 2013 17:24:47 -0400 Subject: [MINC-users] Trouble installing RMINC In-Reply-To: References: Message-ID: It looks like you are missing some of the automagic tools (autoconf, etc). Jason On 2013-04-13, at 5:17 PM, Jonathan DuBois wrote: > Hi Minc Users, > > I am having some trouble installing RMINC on my Mac. I followed the > direction here: https://github.com/mcvaneede/RMINC. The specific commands > and errors are below. Any help would be appreciated. > > Alternatively, is there a minc function to export the values and > coordinates of a minc file to a csv or text file that could imported into > R, manipulated, and written back to a minc file? > > ###################### > :/usr/local$ export R_LIBS=/usr/local/ > :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC > :/usr/local$ cd RMINC > :/usr/local/RMINC$ ./autogen.sh > ./autogen.sh: line 1: aclocal: command not found > ./autogen.sh: line 2: autoconf: command not found > :/usr/local/RMINC$ cd .. > :/usr/local$ sudo R CMD INSTALL RMINC > /Library/Frameworks/R.framework/Versions/3.0/Resources/library > --configure-args='--with-build-path=/usr/local/bic' > Warning: invalid package > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > * installing to library > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > * installing *source* package ?RMINC? ... > ERROR: a 'NAMESPACE' file is required > * removing > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC? > ###################### > > Thanks > Jon DuBois > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From jonathan.m.dubois at gmail.com Sun Apr 14 13:32:34 2013 From: jonathan.m.dubois at gmail.com (Jonathan DuBois) Date: Sun, 14 Apr 2013 13:32:34 -0400 Subject: [MINC-users] MINC-users Digest, Vol 93, Issue 7 In-Reply-To: References: Message-ID: Thanks guys! I installed automake with homebrew and reran the command to install RMINC. It installed and seems to work, although I haven't tested it fully. However, the install process gave the following warnings, is that normal? Jon minc_anova.c: In function ?test_slice_loop?: minc_anova.c:109: warning: assignment from incompatible pointer type minc_anova.c:121: warning: passing argument 4 of ?fill_slice_buffer? from incompatible pointer type minc_anova.c:132: warning: passing argument 3 of ?free_slice_buffer? from incompatible pointer type minc_anova.c:88: warning: unused variable ?num_files? minc_anova.c:86: warning: unused variable ?i? minc_anova.c: In function ?per_voxel_anova?: minc_anova.c:240: warning: passing argument 5 of ?get_indices? from incompatible pointer type minc_anova.c:240: warning: passing argument 6 of ?get_indices? from incompatible pointer type llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/bic/include -Wall -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c minc_reader.c -o minc_reader.o minc_reader.c: In function ?minc2_apply?: minc_reader.c:285: warning: unused variable ?R_fcall? llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/bic/include -Wall -I/usr/local/include -fPIC -mtune=core2 -g -O2 -c modelling_functions.c -o modelling_functions.o modelling_functions.c: In function ?t_test?: modelling_functions.c:104: warning: unused variable ?s_p? modelling_functions.c: In function ?voxel_sum?: modelling_functions.c:241: warning: unused variable ?subjects_per_group? modelling_functions.c: In function ?voxel_lm?: modelling_functions.c:431: warning: implicit declaration of function ?dqrls_? modelling_functions.c:471: warning: implicit declaration of function ?ch2inv_? modelling_functions.c: In function ?minc2_model?: modelling_functions.c:685: warning: assignment discards qualifiers from pointer target type modelling_functions.c:679: warning: unused variable ?index? modelling_functions.c:679: warning: unused variable ?rdf? modelling_functions.c:679: warning: unused variable ?j? modelling_functions.c:679: warning: unused variable ?rank? modelling_functions.c:679: warning: unused variable ?ny? modelling_functions.c:678: warning: unused variable ?resvar? modelling_functions.c:678: warning: unused variable ?rss? modelling_functions.c:678: warning: unused variable ?tol? modelling_functions.c:676: warning: unused variable ?x? modelling_functions.c:676: warning: unused variable ?y? modelling_functions.c:674: warning: unused variable ?R_fcall? modelling_functions.c:667: warning: unused variable ?xn? On Sun, Apr 14, 2013 at 12:00 PM, wrote: > Send MINC-users mailing list submissions to > minc-users at bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > or, via email, send a message with subject or body 'help' to > minc-users-request at bic.mni.mcgill.ca > > You can reach the person managing the list at > minc-users-owner at bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MINC-users digest..." > > > Today's Topics: > > 1. Trouble installing RMINC (Jonathan DuBois) > 2. Re: Trouble installing RMINC (Vladimir S. Fonov) > 3. Re: Trouble installing RMINC (Jason Lerch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 13 Apr 2013 17:17:13 -0400 > From: Jonathan DuBois > To: minc-users at bic.mni.mcgill.ca > Subject: [MINC-users] Trouble installing RMINC > Message-ID: > T6FKHMCKb9x0nR+Q at mail.gmail.com> > Content-Type: text/plain; charset=windows-1252 > > Hi Minc Users, > > I am having some trouble installing RMINC on my Mac. I followed the > direction here: https://github.com/mcvaneede/RMINC. The specific commands > and errors are below. Any help would be appreciated. > > Alternatively, is there a minc function to export the values and > coordinates of a minc file to a csv or text file that could imported into > R, manipulated, and written back to a minc file? > > ###################### > :/usr/local$ export R_LIBS=/usr/local/ > :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC > :/usr/local$ cd RMINC > :/usr/local/RMINC$ ./autogen.sh > ./autogen.sh: line 1: aclocal: command not found > ./autogen.sh: line 2: autoconf: command not found > :/usr/local/RMINC$ cd .. > :/usr/local$ sudo R CMD INSTALL RMINC > /Library/Frameworks/R.framework/Versions/3.0/Resources/library > --configure-args='--with-build-path=/usr/local/bic' > Warning: invalid package > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > * installing to library > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > * installing *source* package ?RMINC? ... > ERROR: a 'NAMESPACE' file is required > * removing > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC? > ###################### > > Thanks > Jon DuBois > > > ------------------------------ > > Message: 2 > Date: Sat, 13 Apr 2013 17:21:02 -0400 > From: "Vladimir S. Fonov" > To: MINC users mailing list > Subject: Re: [MINC-users] Trouble installing RMINC > Message-ID: <5169CC3E.50207 at gmail.com> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Hello, > > > looks like you don't have autoconf/automake installed on your system - > > ./autogen.sh: line 1: aclocal: command not found > > ./autogen.sh: line 2: autoconf: command not found > indicates that these commands are missing > > On 13-04-13 05:17 PM, Jonathan DuBois wrote: > > Hi Minc Users, > > > > I am having some trouble installing RMINC on my Mac. I followed the > > direction here: https://github.com/mcvaneede/RMINC. The specific > commands > > and errors are below. Any help would be appreciated. > > > > Alternatively, is there a minc function to export the values and > > coordinates of a minc file to a csv or text file that could imported into > > R, manipulated, and written back to a minc file? > > > > ###################### > > :/usr/local$ export R_LIBS=/usr/local/ > > :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC > > :/usr/local$ cd RMINC > > :/usr/local/RMINC$ ./autogen.sh > > ./autogen.sh: line 1: aclocal: command not found > > ./autogen.sh: line 2: autoconf: command not found > > :/usr/local/RMINC$ cd .. > > :/usr/local$ sudo R CMD INSTALL RMINC > > /Library/Frameworks/R.framework/Versions/3.0/Resources/library > > --configure-args='--with-build-path=/usr/local/bic' > > Warning: invalid package > > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > > * installing to library > > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > > * installing *source* package ?RMINC? ... > > ERROR: a 'NAMESPACE' file is required > > * removing > > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC? > > > -- > Best regards, > Vladimir S. Fonov ~ vladimir.fonov gmail.com > > > ------------------------------ > > Message: 3 > Date: Sat, 13 Apr 2013 17:24:47 -0400 > From: Jason Lerch > To: MINC users mailing list > Subject: Re: [MINC-users] Trouble installing RMINC > Message-ID: > Content-Type: text/plain; charset="utf-8" > > It looks like you are missing some of the automagic tools (autoconf, etc). > > Jason > > On 2013-04-13, at 5:17 PM, Jonathan DuBois > wrote: > > > Hi Minc Users, > > > > I am having some trouble installing RMINC on my Mac. I followed the > > direction here: https://github.com/mcvaneede/RMINC. The specific > commands > > and errors are below. Any help would be appreciated. > > > > Alternatively, is there a minc function to export the values and > > coordinates of a minc file to a csv or text file that could imported into > > R, manipulated, and written back to a minc file? > > > > ###################### > > :/usr/local$ export R_LIBS=/usr/local/ > > :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC > > :/usr/local$ cd RMINC > > :/usr/local/RMINC$ ./autogen.sh > > ./autogen.sh: line 1: aclocal: command not found > > ./autogen.sh: line 2: autoconf: command not found > > :/usr/local/RMINC$ cd .. > > :/usr/local$ sudo R CMD INSTALL RMINC > > /Library/Frameworks/R.framework/Versions/3.0/Resources/library > > --configure-args='--with-build-path=/usr/local/bic' > > Warning: invalid package > > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > > * installing to library > > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? > > * installing *source* package ?RMINC? ... > > ERROR: a 'NAMESPACE' file is required > > * removing > > ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC? > > ###################### > > > > Thanks > > Jon DuBois > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > ------------------------------ > > _______________________________________________ > MINC-users mailing list > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > End of MINC-users Digest, Vol 93, Issue 7 > ***************************************** > From jason at phenogenomics.ca Mon Apr 15 15:51:28 2013 From: jason at phenogenomics.ca (Jason Lerch) Date: Mon, 15 Apr 2013 15:51:28 -0400 Subject: [MINC-users] MINC-users Digest, Vol 93, Issue 7 In-Reply-To: References: Message-ID: <9B0CF605-4139-47BD-AEC8-2D741CCF527D@phenogenomics.ca> These warnings are indeed "normal" - if I remember they come out in part because some variable are initialized in the R session, which the C compiler does not know about and thus complains. I could be wrong on that part though; anyway, they do appear on every system, not just yours. Jason On 2013-04-14, at 1:32 PM, Jonathan DuBois wrote: > Thanks guys! > > I installed automake with homebrew and reran the command to install RMINC. > It installed and seems to work, although I haven't tested it fully. > However, the install process gave the following warnings, is that normal? > > Jon > > minc_anova.c: In function ?test_slice_loop?: > minc_anova.c:109: warning: assignment from incompatible pointer type > minc_anova.c:121: warning: passing argument 4 of ?fill_slice_buffer? from > incompatible pointer type > minc_anova.c:132: warning: passing argument 3 of ?free_slice_buffer? from > incompatible pointer type > minc_anova.c:88: warning: unused variable ?num_files? > minc_anova.c:86: warning: unused variable ?i? > minc_anova.c: In function ?per_voxel_anova?: > minc_anova.c:240: warning: passing argument 5 of ?get_indices? from > incompatible pointer type > minc_anova.c:240: warning: passing argument 6 of ?get_indices? from > incompatible pointer type > llvm-gcc-4.2 -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/bic/include -Wall -I/usr/local/include -fPIC -mtune=core2 > -g -O2 -c minc_reader.c -o minc_reader.o > minc_reader.c: In function ?minc2_apply?: > minc_reader.c:285: warning: unused variable ?R_fcall? > llvm-gcc-4.2 -arch x86_64 -std=gnu99 > -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG > -I/usr/local/bic/include -Wall -I/usr/local/include -fPIC -mtune=core2 > -g -O2 -c modelling_functions.c -o modelling_functions.o > modelling_functions.c: In function ?t_test?: > modelling_functions.c:104: warning: unused variable ?s_p? > modelling_functions.c: In function ?voxel_sum?: > modelling_functions.c:241: warning: unused variable ?subjects_per_group? > modelling_functions.c: In function ?voxel_lm?: > modelling_functions.c:431: warning: implicit declaration of function > ?dqrls_? > modelling_functions.c:471: warning: implicit declaration of function > ?ch2inv_? > modelling_functions.c: In function ?minc2_model?: > modelling_functions.c:685: warning: assignment discards qualifiers from > pointer target type > modelling_functions.c:679: warning: unused variable ?index? > modelling_functions.c:679: warning: unused variable ?rdf? > modelling_functions.c:679: warning: unused variable ?j? > modelling_functions.c:679: warning: unused variable ?rank? > modelling_functions.c:679: warning: unused variable ?ny? > modelling_functions.c:678: warning: unused variable ?resvar? > modelling_functions.c:678: warning: unused variable ?rss? > modelling_functions.c:678: warning: unused variable ?tol? > modelling_functions.c:676: warning: unused variable ?x? > modelling_functions.c:676: warning: unused variable ?y? > modelling_functions.c:674: warning: unused variable ?R_fcall? > modelling_functions.c:667: warning: unused variable ?xn? > > > On Sun, Apr 14, 2013 at 12:00 PM, wrote: > >> Send MINC-users mailing list submissions to >> minc-users at bic.mni.mcgill.ca >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> or, via email, send a message with subject or body 'help' to >> minc-users-request at bic.mni.mcgill.ca >> >> You can reach the person managing the list at >> minc-users-owner at bic.mni.mcgill.ca >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of MINC-users digest..." >> >> >> Today's Topics: >> >> 1. Trouble installing RMINC (Jonathan DuBois) >> 2. Re: Trouble installing RMINC (Vladimir S. Fonov) >> 3. Re: Trouble installing RMINC (Jason Lerch) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sat, 13 Apr 2013 17:17:13 -0400 >> From: Jonathan DuBois >> To: minc-users at bic.mni.mcgill.ca >> Subject: [MINC-users] Trouble installing RMINC >> Message-ID: >> > T6FKHMCKb9x0nR+Q at mail.gmail.com> >> Content-Type: text/plain; charset=windows-1252 >> >> Hi Minc Users, >> >> I am having some trouble installing RMINC on my Mac. I followed the >> direction here: https://github.com/mcvaneede/RMINC. The specific commands >> and errors are below. Any help would be appreciated. >> >> Alternatively, is there a minc function to export the values and >> coordinates of a minc file to a csv or text file that could imported into >> R, manipulated, and written back to a minc file? >> >> ###################### >> :/usr/local$ export R_LIBS=/usr/local/ >> :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC >> :/usr/local$ cd RMINC >> :/usr/local/RMINC$ ./autogen.sh >> ./autogen.sh: line 1: aclocal: command not found >> ./autogen.sh: line 2: autoconf: command not found >> :/usr/local/RMINC$ cd .. >> :/usr/local$ sudo R CMD INSTALL RMINC >> /Library/Frameworks/R.framework/Versions/3.0/Resources/library >> --configure-args='--with-build-path=/usr/local/bic' >> Warning: invalid package >> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? >> * installing to library >> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? >> * installing *source* package ?RMINC? ... >> ERROR: a 'NAMESPACE' file is required >> * removing >> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC? >> ###################### >> >> Thanks >> Jon DuBois >> >> >> ------------------------------ >> >> Message: 2 >> Date: Sat, 13 Apr 2013 17:21:02 -0400 >> From: "Vladimir S. Fonov" >> To: MINC users mailing list >> Subject: Re: [MINC-users] Trouble installing RMINC >> Message-ID: <5169CC3E.50207 at gmail.com> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> Hello, >> >> >> looks like you don't have autoconf/automake installed on your system - >>> ./autogen.sh: line 1: aclocal: command not found >>> ./autogen.sh: line 2: autoconf: command not found >> indicates that these commands are missing >> >> On 13-04-13 05:17 PM, Jonathan DuBois wrote: >>> Hi Minc Users, >>> >>> I am having some trouble installing RMINC on my Mac. I followed the >>> direction here: https://github.com/mcvaneede/RMINC. The specific >> commands >>> and errors are below. Any help would be appreciated. >>> >>> Alternatively, is there a minc function to export the values and >>> coordinates of a minc file to a csv or text file that could imported into >>> R, manipulated, and written back to a minc file? >>> >>> ###################### >>> :/usr/local$ export R_LIBS=/usr/local/ >>> :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC >>> :/usr/local$ cd RMINC >>> :/usr/local/RMINC$ ./autogen.sh >>> ./autogen.sh: line 1: aclocal: command not found >>> ./autogen.sh: line 2: autoconf: command not found >>> :/usr/local/RMINC$ cd .. >>> :/usr/local$ sudo R CMD INSTALL RMINC >>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library >>> --configure-args='--with-build-path=/usr/local/bic' >>> Warning: invalid package >>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? >>> * installing to library >>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? >>> * installing *source* package ?RMINC? ... >>> ERROR: a 'NAMESPACE' file is required >>> * removing >>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC? >> >> >> -- >> Best regards, >> Vladimir S. Fonov ~ vladimir.fonov gmail.com >> >> >> ------------------------------ >> >> Message: 3 >> Date: Sat, 13 Apr 2013 17:24:47 -0400 >> From: Jason Lerch >> To: MINC users mailing list >> Subject: Re: [MINC-users] Trouble installing RMINC >> Message-ID: >> Content-Type: text/plain; charset="utf-8" >> >> It looks like you are missing some of the automagic tools (autoconf, etc). >> >> Jason >> >> On 2013-04-13, at 5:17 PM, Jonathan DuBois >> wrote: >> >>> Hi Minc Users, >>> >>> I am having some trouble installing RMINC on my Mac. I followed the >>> direction here: https://github.com/mcvaneede/RMINC. The specific >> commands >>> and errors are below. Any help would be appreciated. >>> >>> Alternatively, is there a minc function to export the values and >>> coordinates of a minc file to a csv or text file that could imported into >>> R, manipulated, and written back to a minc file? >>> >>> ###################### >>> :/usr/local$ export R_LIBS=/usr/local/ >>> :/usr/local$ sudo git clone https://github.com/mcvaneede/RMINC.git RMINC >>> :/usr/local$ cd RMINC >>> :/usr/local/RMINC$ ./autogen.sh >>> ./autogen.sh: line 1: aclocal: command not found >>> ./autogen.sh: line 2: autoconf: command not found >>> :/usr/local/RMINC$ cd .. >>> :/usr/local$ sudo R CMD INSTALL RMINC >>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library >>> --configure-args='--with-build-path=/usr/local/bic' >>> Warning: invalid package >>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? >>> * installing to library >>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library? >>> * installing *source* package ?RMINC? ... >>> ERROR: a 'NAMESPACE' file is required >>> * removing >>> ?/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RMINC? >>> ###################### >>> >>> Thanks >>> Jon DuBois >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> >> ------------------------------ >> >> _______________________________________________ >> MINC-users mailing list >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> >> End of MINC-users Digest, Vol 93, Issue 7 >> ***************************************** >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From sylvain at bic.mni.mcgill.ca Tue Apr 16 18:49:47 2013 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Tue, 16 Apr 2013 18:49:47 -0400 (EDT) Subject: [MINC-users] brain-view 0.8 on Ubuntu precise ... Message-ID: Hello Minc-users, has anyone successfuly compiled brain-view (version 0.8) on Ubuntu precise ? I get some undefined references at load time, here's the top of the list: g++ -DQT3_SUPPORT -lQt3Support -L/data/software/BIC/Build/Minc-2/Ubuntu-12.04/install//usr/local/bic/lib -L/usr/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/share/qt4/lib -o brain-view brain-view.o callbacks.o pointInfoWindow.o pointPicker.o brainApp.o brainWidget.o vertStatsFileDialog.o brainEnvironment.o vertstatsForm.o vertexInfo.o screenCaptureForm.o screenCapture.o optionsForm.o options.o rplotformbase.o anatconForm.o anatcon.o RPlot.o extselection.o Rinterface.o pointInfoWindow.moc.o pointPicker.moc.o brainApp.moc.o brainWidget.moc.o vertstatsForm.moc.o vertexInfo.moc.o screenCaptureForm.moc.o screenCapture.moc.o optionsForm.moc.o options.moc.o rplotformbase.moc.o RPlot.moc.o Rinterface.moc.o anatconForm.moc.o anatcon.moc.o -lbicInventor -lCoin -lGL -lSM -lICE -lXmu -lXext -lSM -lICE -lXi -lX11 -loobicpl -lpcre++ -lpcre -lbicpl -lvolume_io2 -lminc2 -lhdf5 -lz -lnetcdf -lm -lSoQt4 -lQtOpenGL -lQtGui -lQtCore -lXmu -lXi -lCoin -lGL -lXext -lSM -lICE -lX11 -ldl -lpthread -lCoin -lGL -lXext -lSM -lICE -lX11 -ldl -lpthread brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x18): undefined reference to `Q3GList::clear()' brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x20): undefined reference to `Q3GList::~Q3GList()' brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x28): undefined reference to `Q3GList::~Q3GList()' brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x30): undefined reference to `Q3PtrCollection::newItem(void*)' brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x40): undefined reference to `Q3GList::compareItems(void*, void*)' brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x48): undefined reference to `Q3GList::read(QDataStream&, void*&)' brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x50): undefined reference to `Q3GList::write(QDataStream&, void*) const' brain-view.o:(.rodata._ZTI7Q3GList[typeinfo for Q3GList]+0x10): undefined reference to `typeinfo for Q3PtrCollection' pointInfoWindow.o: In function `coordinateInfoSet::coordinateInfoSet(QWidget*, char const*)': pointInfoWindow.cc:(.text+0x53): undefined reference to `Q3HBox::Q3HBox(QWidget*, char const*, QFlags)' pointInfoWindow.o: In function `textureInfoSet::textureInfoSet(QWidget*, char const*)': pointInfoWindow.cc:(.text+0x7ff): undefined reference to `Q3HBox::Q3HBox(QWidget*, char const*, QFlags)' pointInfoWindow.o: In function `pointInfoWindow::pointInfoWindow(QWidget*, char const*)': pointInfoWindow.cc:(.text+0xbb4): undefined reference to `Q3VBox::Q3VBox(QWidget*, char const*, QFlags)' pointInfoWindow.o: In function `Q3HBox::~Q3HBox()': pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x13): undefined reference to `vtable for Q3HBox' pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x1f): undefined reference to `vtable for Q3HBox' pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x2b): undefined reference to `Q3Frame::~Q3Frame()' pointInfoWindow.o: In function `Q3VBox::~Q3VBox()': pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x13): undefined reference to `vtable for Q3VBox' pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x1f): undefined reference to `vtable for Q3VBox' ... ideas anyone ? Sylvain From a.janke at gmail.com Tue Apr 16 18:58:50 2013 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 17 Apr 2013 08:58:50 +1000 Subject: [MINC-users] brain-view 0.8 on Ubuntu precise ... In-Reply-To: References: Message-ID: Hi Sylvain, On 17 April 2013 08:49, Sylvain Milot wrote: > has anyone successfuly compiled brain-view (version 0.8) on Ubuntu precise ? Yes. > I get some undefined references at load time, here's the top of > the list: > > pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x13): undefined > reference to `vtable for Q3HBox' > pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x1f): undefined > reference to `vtable for Q3HBox' > pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x2b): undefined > reference to `Q3Frame::~Q3Frame()' > pointInfoWindow.o: In function `Q3VBox::~Q3VBox()': > pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x13): undefined > reference to `vtable for Q3VBox' > pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x1f): undefined > reference to `vtable for Q3VBox' Here is the list of prereq's I used for precise. libnetcdf-dev libhdf5-serial-dev libnetpbm10-dev fftw-dev libgsl0-dev libgetopt-tabular-perl libmni-perllib-perl libxext-dev imagemagick libtext-format-perl freeglut3-dev libsoqt3-dev libxmu-dev libxi-dev imagemagick libtext-format-perl libpcre++0 libpcre3 libsimage-dev libpcre++-dev libqt3-mt-dev qt3-dev-tools Jason might have a more complete list but this is what I have recorded. a From mishkind at gmail.com Tue Apr 16 19:06:15 2013 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Tue, 16 Apr 2013 19:06:15 -0400 Subject: [MINC-users] brain-view 0.8 on Ubuntu precise ... In-Reply-To: References: Message-ID: Hi, After much pain I finally did hack something together on a 64-bit ubuntu precise (12.04) machine. See this thread: http://www.bic.mni.mcgill.ca/pipermail/minc-users/2012-July/003452.html Also, below is the follow up email that I never did send out to the list regarding the final, really ugly hacks to get things working. Hope that at least gives you a place to start...and doesn't send you down the wrong path. mishkin Hi, I forgot to send a follow up email but it turns out I still have some problems with brain-view2. When I was compiling/testing brain-view2 I had done it remotely, using ssh -X into my work computer. All seemed to work fine. Then when i came into work and ran it locally i got this error: opus[~]$ /opt/minc/bin/brain-view2 (brain-view2:5510): GLib-CRITICAL **: PCRE library is compiled without UTF8 support And it just hangs. I tried compiling pcre with utf support and linking against that but i still got the same error. Could be that i didn't link things properly, but I found a work around by looking at the environment variables when I use ssh -X. Turns out I can set DBUS_SESSION_BUS_ADDRESS and it will "work". opus[~]$ DBUS_SESSION_BUS_ADDRESS=unix: /opt/minc/bin/brain-view2 I can load an object file, and I can load an object file with a texture map (thickness.txt), but when I try to load a vertstats file (output from mni.write.vertex.stats in R) I get a core dump: DBUS_SESSION_BUS_ADDRESS=unix: /opt/minc/bin/brain-view2 ../../../../fsaverage/surf/lh.mid.obj lh.thickness.mid.asc.fwhm10.fsaverage.GROUP.vertstats (process:5549): GConf-WARNING **: Client failed to connect to the D-BUS daemon: Server address of type unix was missing argument path or abstract (process:5549): GConf-WARNING **: Client failed to connect to the D-BUS daemon: Server address of type unix was missing argument path or abstract (process:5549): GConf-WARNING **: Client failed to connect to the D-BUS daemon: Server address of type unix was missing argument path or abstract QGtkStyle was unable to detect the current GTK+ theme. Debug. [ MainWindow() ] Settings path 1: "/home/mishkin/.config/MINC/brain-view.conf" Debug. [ MainWindow() ] Settings path 2: "/home/mishkin/.config/MINC/brain-view.ini" Debug. [ MainWindow() ] Application Pid: 5549 Debug. [ initColourbars() ] TextureDir: "/home/mishkin/.config/MINC/textures/" Debug. [ initColourbars() ] Texture file full path: ":/resources/colourbars/sunrise.png" Debug. [ initColourbars() ] Texture file basename: "sunrise" Debug. [ initColourbars() ] Texture file full path: ":/resources/colourbars/hotblue.png" Debug. [ initColourbars() ] Texture file basename: "hotblue" Debug. [ initColourbars() ] Texture file full path: ":/resources/colourbars/spectral.png" Debug. [ initColourbars() ] Texture file basename: "spectral" Debug. [ initColourbars() ] Texture file full path: ":/resources/colourbars/hotred.png" Debug. [ initColourbars() ] Texture file basename: "hotred" Debug. [ initColourbars() ] Texture file full path: ":/resources/colourbars/full_saturation.png" Debug. [ initColourbars() ] Texture file basename: "full_saturation" Debug. [ main ] Loading ... ../../../../fsaverage/surf/lh.mid.obj Loading Polygon object number: 0 Debug: << geometry->loadObj # 0 status = true Debug. [ somethingChanged() ] GRUNKLE Debug. [ main ] Loading ... lh.thickness.mid.asc.fwhm10.fsaverage.GROUP.vertstats Debug. [ fillTextureVector() ] Using texture directory: "/home/mishkin/.config/MINC/textures/" Debug. [ fillTextureVector() ] Texture full filename: "/home/mishkin/.config/MINC/textures//full_saturation.png" Debug. [ fillTextureVector() ] Texture full filename: "/home/mishkin/.config/MINC/textures//hotblue.png" Debug. [ fillTextureVector() ] Texture full filename: "/home/mishkin/.config/MINC/textures//hotred.png" Debug. [ fillTextureVector() ] Texture full filename: "/home/mishkin/.config/MINC/textures//spectral.png" Debug. [ fillTextureVector() ] Texture full filename: "/home/mishkin/.config/MINC/textures//sunrise.png" terminate called after throwing an instance of 'mniVertstatsFile::InvalidColumnError' Aborted (core dumped) I tried looking into the error a bit, and i think it is from oobicpl but I'm not sure, and I had to abandon the project; Louis didn't like me working on something other than my thesis, and despite the ugliness of the hacks, i can visualize what i need to. All that to say that this minc-users email might come in handy for someone else who might get the same errors, but it certainly isn't a foolproof recipe to get brain-view2 working. On Tue, Apr 16, 2013 at 6:49 PM, Sylvain Milot wrote: > > Hello Minc-users, > > has anyone successfuly compiled brain-view (version 0.8) on Ubuntu precise ? > > I get some undefined references at load time, here's the top of > the list: > > g++ -DQT3_SUPPORT -lQt3Support > -L/data/software/BIC/Build/Minc-2/Ubuntu-12.04/install//usr/local/bic/lib > -L/usr/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -L/usr/share/qt4/lib -o > brain-view brain-view.o callbacks.o pointInfoWindow.o pointPicker.o > brainApp.o brainWidget.o vertStatsFileDialog.o brainEnvironment.o > vertstatsForm.o vertexInfo.o screenCaptureForm.o screenCapture.o > optionsForm.o options.o rplotformbase.o anatconForm.o anatcon.o RPlot.o > extselection.o Rinterface.o pointInfoWindow.moc.o pointPicker.moc.o > brainApp.moc.o brainWidget.moc.o vertstatsForm.moc.o vertexInfo.moc.o > screenCaptureForm.moc.o screenCapture.moc.o optionsForm.moc.o options.moc.o > rplotformbase.moc.o RPlot.moc.o Rinterface.moc.o anatconForm.moc.o > anatcon.moc.o -lbicInventor -lCoin -lGL -lSM -lICE -lXmu -lXext -lSM -lICE > -lXi -lX11 -loobicpl -lpcre++ -lpcre -lbicpl -lvolume_io2 -lminc2 -lhdf5 > -lz -lnetcdf -lm -lSoQt4 -lQtOpenGL -lQtGui -lQtCore -lXmu -lXi -lCoin -lGL > -lXext -lSM -lICE -lX11 -ldl -lpthread -lCoin -lGL -lXext -lSM -lICE -lX11 > -ldl -lpthread brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x18): > undefined reference to `Q3GList::clear()' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x20): undefined > reference to `Q3GList::~Q3GList()' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x28): undefined > reference to `Q3GList::~Q3GList()' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x30): undefined > reference to `Q3PtrCollection::newItem(void*)' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x40): undefined > reference to `Q3GList::compareItems(void*, void*)' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x48): undefined > reference to `Q3GList::read(QDataStream&, void*&)' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x50): undefined > reference to `Q3GList::write(QDataStream&, void*) const' > brain-view.o:(.rodata._ZTI7Q3GList[typeinfo for Q3GList]+0x10): undefined > reference to `typeinfo for Q3PtrCollection' > pointInfoWindow.o: In function > `coordinateInfoSet::coordinateInfoSet(QWidget*, char const*)': > pointInfoWindow.cc:(.text+0x53): undefined reference to > `Q3HBox::Q3HBox(QWidget*, char const*, QFlags)' > pointInfoWindow.o: In function `textureInfoSet::textureInfoSet(QWidget*, > char const*)': > pointInfoWindow.cc:(.text+0x7ff): undefined reference to > `Q3HBox::Q3HBox(QWidget*, char const*, QFlags)' > pointInfoWindow.o: In function `pointInfoWindow::pointInfoWindow(QWidget*, > char const*)': > pointInfoWindow.cc:(.text+0xbb4): undefined reference to > `Q3VBox::Q3VBox(QWidget*, char const*, QFlags)' > pointInfoWindow.o: In function `Q3HBox::~Q3HBox()': > pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x13): undefined > reference to `vtable for Q3HBox' > pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x1f): undefined > reference to `vtable for Q3HBox' > pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x2b): undefined > reference to `Q3Frame::~Q3Frame()' > pointInfoWindow.o: In function `Q3VBox::~Q3VBox()': > pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x13): undefined > reference to `vtable for Q3VBox' > pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x1f): undefined > reference to `vtable for Q3VBox' > ... > > ideas anyone ? > > Sylvain > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From claude at bic.mni.mcgill.ca Tue Apr 16 19:21:30 2013 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Tue, 16 Apr 2013 19:21:30 -0400 Subject: [MINC-users] brain-view 0.8 on Ubuntu precise ... In-Reply-To: Message-ID: <201304162321.r3GNLUiT023519@agrippa.bic.mni.mcgill.ca> Hi, Beware that there is the old brain-view-0.8.0 and there is Jason's new brain-view2 (what Mishkin is talking about). The former is based on Coin3d, Qt3/Qt4, simage. For the old brain-view-0.8.0: @echo "For brain-view, adding the following:" @echo " NEW WAY: libsimage-dev libsoqt4-dev libqt4 I recently added the compilation of SOQT as part of my build. Make that SoQt-1.4.2a. $(SOQT): $(SOQT_UNTAR) cd ${SOURCE_DIR}/${SOQT_PACKAGE} ; \ QTINC=/usr/lib64/qt4/include ; export QTINC ; \ QTDIR=/usr/lib64/qt4 ; export QTDIR ; \ QTILIB=/usr/lib64/qt4/lib64 ; export QTLIB ; \ export PATH=/usr/lib64/qt4/bin:${PATH} ; \ if [ ! -e Makefile ] ; then \ ./configure --prefix=$(PREFIX_PATH) --with-build-path=$(BUILD_PATH); \ fi ; \ ${MAKE}; ${MAKE} install $(BRAINVIEW): $(BRAINVIEW_UNTAR) $(M4_UNTAR) $(LIBBICINVENTOR) $(SOQT) cd ${SOURCE_DIR}/${BRAINVIEW_PACKAGE}/ ; \ if [ ! -d m4 ] ; then ln -fs ../m4 ./m4 ;fi ; \ if [ ! -e Makefile ] ; then \ rm -rf textures/brain-view-config ; \ rm -rf src/brainEnvironment.cc ; \ ./configure $(MINC_FLAG) --disable-shared --prefix=$(PREFIX_PATH) --with-build-path=$(BUILD_PATH) CFLAGS='${CFLAGS} -DQT3_SUPPORT -I/usr/lib64/qt4/include' CPPFLAGS='${CPPFLAGS} -DQT3_SUPPORT -I/usr/lib64/qt4/include' CXXFLAGS='${CXXFLAGS} -DQT3_SUPPORT -I/usr/lib64/qt4/include' LDFLAGS='${LDFLAGS} -L/usr/lib64/qt4/lib64 -lQt3Support'; \ fi ; \ ${MAKE}; ${MAKE} install Claude From sylvain at bic.mni.mcgill.ca Tue Apr 16 20:58:06 2013 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Tue, 16 Apr 2013 20:58:06 -0400 (EDT) Subject: [MINC-users] brain-view 0.8 on Ubuntu precise ... In-Reply-To: References: Message-ID: Hello Andrew, On Wed, 17 Apr 2013, Andrew Janke wrote: > Hi Sylvain, > > On 17 April 2013 08:49, Sylvain Milot wrote: >> has anyone successfuly compiled brain-view (version 0.8) on Ubuntu precise ? > > Yes. > >> I get some undefined references at load time, here's the top of >> the list: >> >> pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x13): undefined >> reference to `vtable for Q3HBox' >> pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x1f): undefined >> reference to `vtable for Q3HBox' >> pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x2b): undefined >> reference to `Q3Frame::~Q3Frame()' >> pointInfoWindow.o: In function `Q3VBox::~Q3VBox()': >> pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x13): undefined >> reference to `vtable for Q3VBox' >> pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x1f): undefined >> reference to `vtable for Q3VBox' > > Here is the list of prereq's I used for precise. > > libnetcdf-dev libhdf5-serial-dev libnetpbm10-dev fftw-dev libgsl0-dev > libgetopt-tabular-perl libmni-perllib-perl libxext-dev imagemagick > libtext-format-perl freeglut3-dev libsoqt3-dev libxmu-dev libxi-dev > imagemagick libtext-format-perl libpcre++0 libpcre3 libsimage-dev > libpcre++-dev libqt3-mt-dev qt3-dev-tools > > Jason might have a more complete list but this is what I have recorded. I already have all those packages, except for libsoqt3-dev, which AFAICS is not part of Ubuntu precise ... I have ii libsoqt-dev-common 1.5.0-2 ii libsoqt4-20 1.5.0-2 ii libsoqt4-dev 1.5.0-2 If you say that you managed to compile it, then there's hope! I must be overlooking something ... Thanks, Sylvain From a.janke at gmail.com Tue Apr 16 21:10:18 2013 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 17 Apr 2013 11:10:18 +1000 Subject: [MINC-users] brain-view 0.8 on Ubuntu precise ... In-Reply-To: References: Message-ID: > I already have all those packages, except for libsoqt3-dev, which AFAICS > is not part of Ubuntu precise ... I have > > ii libsoqt-dev-common 1.5.0-2 > ii libsoqt4-20 1.5.0-2 > ii libsoqt4-dev 1.5.0-2 > > If you say that you managed to compile it, then there's hope! I must be > overlooking > something ... Hrm, this brings back memories. As I recall I used a backported package to get it all to work. For some reason I also made this: http://httpd.cai.uq.edu.au/~rotor/quarter-1.0.0-1maverick_amd64.deb That also works on precise but can't remember what it was for again (brainview or something else like postf). I could find no package for it anywhere so made my own. a From claude at bic.mni.mcgill.ca Tue Apr 16 23:00:35 2013 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Tue, 16 Apr 2013 23:00:35 -0400 Subject: [MINC-users] brain-view 0.8 on Ubuntu precise ... In-Reply-To: Message-ID: <201304170300.r3H30ZRq005397@agrippa.bic.mni.mcgill.ca> Hi all, Sylvain gave me access to a Ubuntu precise machine and I managed to link brain-view-0.8.0. Some notes (features/bugs): - I had to repeat the link by appending -lQt3Support at the end of the link line. This is gcc 4.6. Maybe the order in which -lQt3Support is listed matters for this compiler. A mystery... Try with an old compiler??? - I had to set the proper include path for Qt4 (not the one below), but that's a minor detail. - the configure skips the check for BicInventor (and oobicpl). I don't know why. Maybe I have to re-run autogen.sh to upgrade the building scripts to the version of autoconf on the system. Maybe fixing this check for BicInventor will fix the link problem. Anyway, it linked. Claude > has anyone successfuly compiled brain-view (version 0.8) on Ubuntu precise = > ? > > I get some undefined references at load time, here's the top of > the list: > > g++ -DQT3_SUPPORT -lQt3Support -L/data/software/BIC/Build/Minc-2/Ubuntu-1= > 2.04/install//usr/local/bic/lib -L/usr/lib -Wl,-Bsymbolic-functions -Wl,-z= > ,relro -L/usr/share/qt4/lib -o brain-view brain-view.o callbacks.o pointI= > nfoWindow.o pointPicker.o brainApp.o brainWidget.o vertStatsFileDialog.o br= > ainEnvironment.o vertstatsForm.o vertexInfo.o screenCaptureForm.o screenCap= > ture.o optionsForm.o options.o rplotformbase.o anatconForm.o anatcon.o RPlo= > t.o extselection.o Rinterface.o pointInfoWindow.moc.o pointPicker.moc.o bra= > inApp.moc.o brainWidget.moc.o vertstatsForm.moc.o vertexInfo.moc.o screenCa= > ptureForm.moc.o screenCapture.moc.o optionsForm.moc.o options.moc.o rplotfo= > rmbase.moc.o RPlot.moc.o Rinterface.moc.o anatconForm.moc.o anatcon.moc.o = > -lbicInventor -lCoin -lGL -lSM -lICE -lXmu -lXext -lSM -lICE -lXi -lX11 -= > loobicpl -lpcre++ -lpcre -lbicpl -lvolume_io2 -lminc2 -lhdf5 -lz -lnetcdf -= > lm -lSoQt4 -lQtOpenGL -lQtGui -lQtCore -lXmu -lXi -lCoin -lGL -lXext -lSM -= > lICE -lX11 -ldl -lpthread -lCoin -lGL -lXext -lSM -lICE -lX11 -ldl -lpthrea= > d=20 > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x18): undefined ref= > erence to `Q3GList::clear()' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x20): undefined ref= > erence to `Q3GList::~Q3GList()' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x28): undefined ref= > erence to `Q3GList::~Q3GList()' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x30): undefined ref= > erence to `Q3PtrCollection::newItem(void*)' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x40): undefined ref= > erence to `Q3GList::compareItems(void*, void*)' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x48): undefined ref= > erence to `Q3GList::read(QDataStream&, void*&)' > brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x50): undefined ref= > erence to `Q3GList::write(QDataStream&, void*) const' > brain-view.o:(.rodata._ZTI7Q3GList[typeinfo for Q3GList]+0x10): undefined r= > eference to `typeinfo for Q3PtrCollection' > pointInfoWindow.o: In function `coordinateInfoSet::coordinateInfoSet(QWidge= > t*, char const*)': > pointInfoWindow.cc:(.text+0x53): undefined reference to `Q3HBox::Q3HBox(QWi= > dget*, char const*, QFlags)' > pointInfoWindow.o: In function `textureInfoSet::textureInfoSet(QWidget*, ch= > ar const*)': > pointInfoWindow.cc:(.text+0x7ff): undefined reference to `Q3HBox::Q3HBox(QW= > idget*, char const*, QFlags)' > pointInfoWindow.o: In function `pointInfoWindow::pointInfoWindow(QWidget*, = > char const*)': > pointInfoWindow.cc:(.text+0xbb4): undefined reference to `Q3VBox::Q3VBox(QW= > idget*, char const*, QFlags)' > pointInfoWindow.o: In function `Q3HBox::~Q3HBox()': > pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x13): undefined r= > eference to `vtable for Q3HBox' > pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x1f): undefined r= > eference to `vtable for Q3HBox' > pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x2b): undefined r= > eference to `Q3Frame::~Q3Frame()' > pointInfoWindow.o: In function `Q3VBox::~Q3VBox()': > pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x13): undefined r= > eference to `vtable for Q3VBox' > pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x1f): undefined r= > eference to `vtable for Q3VBox' > =2E.. > > ideas anyone ? > > Sylvain > ---830177870-344973567-1366152486=:22420 > Content-Type: text/plain; charset="us-ascii" > MIME-Version: 1.0 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > ---830177870-344973567-1366152486=:22420-- > From sylvain at bic.mni.mcgill.ca Wed Apr 17 08:22:48 2013 From: sylvain at bic.mni.mcgill.ca (Sylvain Milot) Date: Wed, 17 Apr 2013 08:22:48 -0400 (EDT) Subject: [MINC-users] brain-view 0.8 on Ubuntu precise ... In-Reply-To: <201304170300.r3H30ZRq005397@agrippa.bic.mni.mcgill.ca> References: <201304170300.r3H30ZRq005397@agrippa.bic.mni.mcgill.ca> Message-ID: Good morning, so as Claude said, appending -lQt3Support at the end of the link line worked for brain-view and gcc 4.6. using libnetpbm10-dev under Ubuntu precise breaks things for some reason but libnetpbm9-dev works. Packages affected here are bicpl, conglomerate and likely Display as well. I also tried with gcc version 4.4 (instead of 4.6) and that worked as well. Thanks to all! Sylvain On Tue, 16 Apr 2013, Claude LEPAGE wrote: > Hi all, > > Sylvain gave me access to a Ubuntu precise machine and I managed > to link brain-view-0.8.0. Some notes (features/bugs): > - I had to repeat the link by appending -lQt3Support at the end > of the link line. This is gcc 4.6. Maybe the order in which > -lQt3Support is listed matters for this compiler. A mystery... > Try with an old compiler??? > - I had to set the proper include path for Qt4 (not the one below), > but that's a minor detail. > - the configure skips the check for BicInventor (and oobicpl). > I don't know why. Maybe I have to re-run autogen.sh to upgrade > the building scripts to the version of autoconf on the system. > Maybe fixing this check for BicInventor will fix the link problem. > > Anyway, it linked. > > Claude > >> has anyone successfuly compiled brain-view (version 0.8) on Ubuntu precise = >> ? >> >> I get some undefined references at load time, here's the top of >> the list: >> >> g++ -DQT3_SUPPORT -lQt3Support -L/data/software/BIC/Build/Minc-2/Ubuntu-1= >> 2.04/install//usr/local/bic/lib -L/usr/lib -Wl,-Bsymbolic-functions -Wl,-z= >> ,relro -L/usr/share/qt4/lib -o brain-view brain-view.o callbacks.o pointI= >> nfoWindow.o pointPicker.o brainApp.o brainWidget.o vertStatsFileDialog.o br= >> ainEnvironment.o vertstatsForm.o vertexInfo.o screenCaptureForm.o screenCap= >> ture.o optionsForm.o options.o rplotformbase.o anatconForm.o anatcon.o RPlo= >> t.o extselection.o Rinterface.o pointInfoWindow.moc.o pointPicker.moc.o bra= >> inApp.moc.o brainWidget.moc.o vertstatsForm.moc.o vertexInfo.moc.o screenCa= >> ptureForm.moc.o screenCapture.moc.o optionsForm.moc.o options.moc.o rplotfo= >> rmbase.moc.o RPlot.moc.o Rinterface.moc.o anatconForm.moc.o anatcon.moc.o = >> -lbicInventor -lCoin -lGL -lSM -lICE -lXmu -lXext -lSM -lICE -lXi -lX11 -= >> loobicpl -lpcre++ -lpcre -lbicpl -lvolume_io2 -lminc2 -lhdf5 -lz -lnetcdf -= >> lm -lSoQt4 -lQtOpenGL -lQtGui -lQtCore -lXmu -lXi -lCoin -lGL -lXext -lSM -= >> lICE -lX11 -ldl -lpthread -lCoin -lGL -lXext -lSM -lICE -lX11 -ldl -lpthrea= >> d=20 >> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x18): undefined ref= >> erence to `Q3GList::clear()' >> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x20): undefined ref= >> erence to `Q3GList::~Q3GList()' >> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x28): undefined ref= >> erence to `Q3GList::~Q3GList()' >> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x30): undefined ref= >> erence to `Q3PtrCollection::newItem(void*)' >> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x40): undefined ref= >> erence to `Q3GList::compareItems(void*, void*)' >> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x48): undefined ref= >> erence to `Q3GList::read(QDataStream&, void*&)' >> brain-view.o:(.rodata._ZTV7Q3GList[vtable for Q3GList]+0x50): undefined ref= >> erence to `Q3GList::write(QDataStream&, void*) const' >> brain-view.o:(.rodata._ZTI7Q3GList[typeinfo for Q3GList]+0x10): undefined r= >> eference to `typeinfo for Q3PtrCollection' >> pointInfoWindow.o: In function `coordinateInfoSet::coordinateInfoSet(QWidge= >> t*, char const*)': >> pointInfoWindow.cc:(.text+0x53): undefined reference to `Q3HBox::Q3HBox(QWi= >> dget*, char const*, QFlags)' >> pointInfoWindow.o: In function `textureInfoSet::textureInfoSet(QWidget*, ch= >> ar const*)': >> pointInfoWindow.cc:(.text+0x7ff): undefined reference to `Q3HBox::Q3HBox(QW= >> idget*, char const*, QFlags)' >> pointInfoWindow.o: In function `pointInfoWindow::pointInfoWindow(QWidget*, = >> char const*)': >> pointInfoWindow.cc:(.text+0xbb4): undefined reference to `Q3VBox::Q3VBox(QW= >> idget*, char const*, QFlags)' >> pointInfoWindow.o: In function `Q3HBox::~Q3HBox()': >> pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x13): undefined r= >> eference to `vtable for Q3HBox' >> pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x1f): undefined r= >> eference to `vtable for Q3HBox' >> pointInfoWindow.cc:(.text._ZN6Q3HBoxD2Ev[_ZN6Q3HBoxD5Ev]+0x2b): undefined r= >> eference to `Q3Frame::~Q3Frame()' >> pointInfoWindow.o: In function `Q3VBox::~Q3VBox()': >> pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x13): undefined r= >> eference to `vtable for Q3VBox' >> pointInfoWindow.cc:(.text._ZN6Q3VBoxD2Ev[_ZN6Q3VBoxD5Ev]+0x1f): undefined r= >> eference to `vtable for Q3VBox' >> =2E.. >> >> ideas anyone ? >> >> Sylvain >> ---830177870-344973567-1366152486=:22420 >> Content-Type: text/plain; charset="us-ascii" >> MIME-Version: 1.0 >> Content-Transfer-Encoding: 7bit >> Content-Disposition: inline >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> >> ---830177870-344973567-1366152486=:22420-- >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From andrew at biospective.com Wed Apr 17 11:14:14 2013 From: andrew at biospective.com (Andrew Wood) Date: Wed, 17 Apr 2013 11:14:14 -0400 Subject: [MINC-users] Volumes containing NaN and mincresample Message-ID: Hi All, I've been running into trouble resampling an image in which there are voxels that carry no meaning. It is essentially a masked image, where meaningful data is anything non-zero. When I resample the image, the meaningless zeros are treated as real data for interpolation and leak into the image (for interpolants other than nearest neighbour). Of course there's nothing special about zero, so I tried this: $ minccalc -expression 'A[0] < 1e-5 ? NaN : A[0]' zeros.mnc NaNs.mnc When I resample NaNs.mnc, I still end up with meaningless voxels leaking into the image. How are NaNs represented in the minc world? It looks like they're simply stored as its slice's minimum value: $ mincextract -start 0,0,0 -count 1,1,1 NaNs.mnc 1.2451361867704378028 $ mincinfo -varvalue image-min NaNs.mnc | head -n 1 1.245136186770423592 Should mincresample treats the NaNs generated by minccalc as real values? Is there a way to persuade mincresample interpolants to ignore a specific value (i.e. NaN)? Thanks, Andrew From sorench at gmail.com Wed Apr 17 13:10:47 2013 From: sorench at gmail.com (Soren Christensen) Date: Wed, 17 Apr 2013 10:10:47 -0700 Subject: [MINC-users] Volumes containing NaN and mincresample In-Reply-To: References: Message-ID: Hi Andrew, I can directly answer your question but this is something I have been dealing with too. So you have a region with "valid" values and a NaN valued region. What do you want to happen in terms of interpolation at the interface between these two regions? That anything "contaminated" by NaN is set to NaN or that the interpolated value excludes NaNs from the neighborhood? In both cases I believe you can achieve this by transforming a [1/0] mask (as float using non-nearest IP) and then use that result as an indicator of what was contaminated by exterior contributions and how much. You can then adapt you image based on this. Soren On Wed, Apr 17, 2013 at 8:14 AM, Andrew Wood wrote: > Hi All, > > I've been running into trouble resampling an image in which there are > voxels that carry no meaning. It is essentially a masked image, where > meaningful data is anything non-zero. When I resample the image, the > meaningless zeros are treated as real data for interpolation and leak into > the image (for interpolants other than nearest neighbour). > > Of course there's nothing special about zero, so I tried this: > > $ minccalc -expression 'A[0] < 1e-5 ? NaN : A[0]' zeros.mnc NaNs.mnc > > When I resample NaNs.mnc, I still end up with meaningless voxels leaking > into the image. > > How are NaNs represented in the minc world? It looks like they're simply > stored as its slice's minimum value: > > $ mincextract -start 0,0,0 -count 1,1,1 NaNs.mnc > 1.2451361867704378028 > > $ mincinfo -varvalue image-min NaNs.mnc | head -n 1 > 1.245136186770423592 > > Should mincresample treats the NaNs generated by minccalc as real values? > Is there a way to persuade mincresample interpolants to ignore a specific > value (i.e. NaN)? > > Thanks, > Andrew > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From peter.neelin at gmail.com Wed Apr 17 19:19:09 2013 From: peter.neelin at gmail.com (Peter Neelin) Date: Wed, 17 Apr 2013 19:19:09 -0400 Subject: [MINC-users] Volumes containing NaN and mincresample In-Reply-To: References: Message-ID: On Apr 17, 2013 11:15 AM, "Andrew Wood" wrote: > How are NaNs represented in the minc world? It looks like they're simply > stored as its slice's minimum value: They are represented as values outside of the valid range. If you have a representation with a valid range that uses all possible values, then you cannot accurately represent an invalid value (e.g. byte data in range 0 to 255). So the first step is to create a minc file the possibility of storing invalid values with something like short values in the range -32000 to 32000 (for example). When using mincresample, you must specify -fill in order to get invalid values out (when any of the contributing voxels is invalid). By default, zero is used (real value zero). You can also specify a real value to insert into those voxels with -fillvalue. Peter -- Peter Neelin peter.neelin at gmail.com