From redoute at cermep.fr  Wed Jun  7 10:51:01 2017
From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=)
Date: Wed, 7 Jun 2017 16:51:01 +0200
Subject: [MINC-users] mincresample -like problem
Message-ID: <58c61418-f37f-bdff-af90-d8b7f67860be@cermep.fr>

Hi all,

here is the problem we are facing with:

1. dcm2mnc DICOM to TEP_DYN.mnc

2. mincaverage  -avgdim time TEP_DYN.mnc TEP_sum.mnc

3. mnc2nii TEP_sum.mnc TEP_sum.nii

3. we use SPM to coregister TEP_sum.nii with MRI, segment MRI and then 
push ATLAS.nii in TEP_sum space

4. at this point: ATLAS.nii and TEP_sum.nii are well coregistred when 
checking with register

5. nii2mnc -byte ATLAS.nii ATLAS.mnc

6. then we need to resample ATLAS.mnc:

     mincresample -verbose -nearest_neighbour -byte -like TEP_sum.mnc 
ATLAS.mnc ATLAS_Res.mnc

the problem is at this step:

we get warnings:

> WARN: Irregular dimension in file TEP_sum.mnc contains non-monotonic 
> or repeated values.
> WARN: Something is wrong with the irregular dimension in file TEP_sum.mnc.
>       Substituting a step size of 1.0.
> WARN: Irregular dimension in file EP_sum.mnc contains non-monotonic or 
> repeated values.
> WARN: Something is wrong with the irregular dimension in file EP_sum.mnc.
>       Substituting a step size of 1.0.
> WARN: Irregular dimension in file EP_sum.mnc contains non-monotonic or 
> repeated values.
> WARN: Something is wrong with the irregular dimension in file EP_sum.mnc.
>       Substituting a step size of 1.0.
and the resulting ATLAS_Res.mnc is not coregistred with TEP_sum.mnc

Any ideas n what is wrong with our reference image?

thank you

Jerome




From bert at phalarope.com  Wed Jun  7 11:08:15 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Wed, 7 Jun 2017 11:08:15 -0400
Subject: [MINC-users] mincresample -like problem
In-Reply-To: <58c61418-f37f-bdff-af90-d8b7f67860be@cermep.fr>
References: <58c61418-f37f-bdff-af90-d8b7f67860be@cermep.fr>
Message-ID: <CAAd5DeT-bgNZF4F9RwjFbwJYhf0v2wex3ZqBb33Zqsj=Ep7dPQ@mail.gmail.com>

Hi Jerome,

I'm not sure. Those warnings may not be telling us anything important. Does
the output of mincresample look good?

Can you send the output of mincheader for TEP_sum.mnc?

    -bert

On Wed, Jun 7, 2017 at 10:51 AM, J?r?me Redout? <redoute at cermep.fr> wrote:

> Hi all,
>
> here is the problem we are facing with:
>
> 1. dcm2mnc DICOM to TEP_DYN.mnc
>
> 2. mincaverage  -avgdim time TEP_DYN.mnc TEP_sum.mnc
>
> 3. mnc2nii TEP_sum.mnc TEP_sum.nii
>
> 3. we use SPM to coregister TEP_sum.nii with MRI, segment MRI and then
> push ATLAS.nii in TEP_sum space
>
> 4. at this point: ATLAS.nii and TEP_sum.nii are well coregistred when
> checking with register
>
> 5. nii2mnc -byte ATLAS.nii ATLAS.mnc
>
> 6. then we need to resample ATLAS.mnc:
>
>     mincresample -verbose -nearest_neighbour -byte -like TEP_sum.mnc
> ATLAS.mnc ATLAS_Res.mnc
>
> the problem is at this step:
>
> we get warnings:
>
> WARN: Irregular dimension in file TEP_sum.mnc contains non-monotonic or
>> repeated values.
>> WARN: Something is wrong with the irregular dimension in file TEP_sum.mnc.
>>       Substituting a step size of 1.0.
>> WARN: Irregular dimension in file EP_sum.mnc contains non-monotonic or
>> repeated values.
>> WARN: Something is wrong with the irregular dimension in file EP_sum.mnc.
>>       Substituting a step size of 1.0.
>> WARN: Irregular dimension in file EP_sum.mnc contains non-monotonic or
>> repeated values.
>> WARN: Something is wrong with the irregular dimension in file EP_sum.mnc.
>>       Substituting a step size of 1.0.
>>
> and the resulting ATLAS_Res.mnc is not coregistred with TEP_sum.mnc
>
> Any ideas n what is wrong with our reference image?
>
> thank you
>
> Jerome
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From redoute at cermep.fr  Wed Jun  7 11:21:56 2017
From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=)
Date: Wed, 7 Jun 2017 17:21:56 +0200
Subject: [MINC-users] mincresample -like problem
In-Reply-To: <CAAd5DeT-bgNZF4F9RwjFbwJYhf0v2wex3ZqBb33Zqsj=Ep7dPQ@mail.gmail.com>
References: <58c61418-f37f-bdff-af90-d8b7f67860be@cermep.fr>
	<CAAd5DeT-bgNZF4F9RwjFbwJYhf0v2wex3ZqBb33Zqsj=Ep7dPQ@mail.gmail.com>
Message-ID: <180b98fd-4719-5a76-3f7d-6495f124dd12@cermep.fr>

Hi Robert,

the output of mincresample is not coregistered anymore with previous files

here is the output of mincheader:

> mincheader BENSU_DPN_DYN_37F_sum.mnc
> hdf5 BENSU_DPN_DYN_37F_sum {
> dimensions:
>     xspace = 256 ;
>     yspace = 256 ;
>     zspace = 109 ;
> variables:
>     short image(zspace, yspace, xspace) ;
>         image:version = "MINC Version    1.0" ;
>         image:vartype = "group________" ;
>         image:valid_range = 0., 65535. ;
>         image:varid = "MINC standard variable" ;
>         image:complete = "true_" ;
>         image:dimorder = "zspace,yspace,xspace" ;
>         image:signtype = "unsigned" ;
>     double image-min(zspace) ;
>         image-min:version = "MINC Version    1.0" ;
>         image-min:vartype = "var_attribute" ;
>         image-min:varid = "MINC standard variable" ;
>         image-min:dimorder = "zspace" ;
>     double image-max(zspace) ;
>         image-max:version = "MINC Version    1.0" ;
>         image-max:vartype = "var_attribute" ;
>         image-max:varid = "MINC standard variable" ;
>         image-max:dimorder = "zspace" ;
>     double xspace ;
>         xspace:version = "MINC Version    1.0" ;
>         xspace:spacetype = "native____" ;
>         xspace:vartype = "dimension____" ;
>         xspace:start = -135. ;
>         xspace:spacing = "irregular" ;
>         xspace:alignment = "centre" ;
>         xspace:direction_cosines = 1., 0., -0. ;
>         xspace:comments = "X increases from patient left to right" ;
>         xspace:varid = "MINC standard variable" ;
>         xspace:length = 256 ;
>         xspace:step = 1.06063 ;
>     double yspace ;
>         yspace:version = "MINC Version    1.0" ;
>         yspace:spacetype = "native____" ;
>         yspace:vartype = "dimension____" ;
>         yspace:start = -135. ;
>         yspace:spacing = "irregular" ;
>         yspace:alignment = "centre" ;
>         yspace:direction_cosines = 0., 1., -0. ;
>         yspace:comments = "Y increases from patient posterior to 
> anterior" ;
>         yspace:varid = "MINC standard variable" ;
>         yspace:length = 256 ;
>         yspace:step = 1.06063 ;
>     double zspace ;
>         zspace:version = "MINC Version    1.0" ;
>         zspace:spacetype = "native____" ;
>         zspace:vartype = "dimension____" ;
>         zspace:start = 127. ;
>         zspace:spacing = "irregular" ;
>         zspace:alignment = "centre" ;
>         zspace:direction_cosines = 0., 0., 1. ;
>         zspace:comments = "Z increases from patient inferior to 
> superior" ;
>         zspace:varid = "MINC standard variable" ;
>         zspace:length = 109 ;
>         zspace:step = -2.027 ;
>     int acquisition ;
>         acquisition:version = "MINC Version    1.0" ;
>         acquisition:acquisition_id = "7" ;
>         acquisition:vartype = "group________" ;
>         acquisition:slice_thickness = 2.027 ;
>         acquisition:injection_route = "\ufffd\ufffd@" ;
>         acquisition:injection_minute = 0 ;
>         acquisition:window_width = 1. ;
>         acquisition:series_time = "143111.000000 " ;
>         acquisition:injection_dose = 6.95309811585881e-310 ;
>         acquisition:num_dyn_scans = 0. ;
>         acquisition:injection_seconds = 0. ;
>         acquisition:series_description = "DIPRE_DYN_UHD_12_21_Z3_256" ;
>         acquisition:delay_in_TR = 0. ;
>         acquisition:acquisition_time = "143111.000004 " ;
>         acquisition:comments = "AC CT Brain, Volume Scaled" ;
>         acquisition:image_time = "132439.593000 " ;
>         acquisition:injection_day = 0 ;
>         acquisition:tracer = "YNr" ;
>         acquisition:injection_hour = 0 ;
>         acquisition:radionuclide_halflife = 6.95098988200896e-310 ;
>         acquisition:positron_fraction = 6.95098865937855e-310 ;
>         acquisition:injection_year = 0 ;
>         acquisition:varid = "MINC standard variable" ;
>         acquisition:injection_volume = 6.95098935489284e-310 ;
>         acquisition:dose_units = "Bq" ;
>         acquisition:injection_time = "\b\ufffd\ufffd\ufffd" ;
>         acquisition:image_type = "ORIGINAL\\PRIMARY" ;
>         acquisition:start_time = "20151105 135819.250000 " ;
>         acquisition:window_center = 0. ;
>         acquisition:injection_month = 0 ;
>     int dicom_0x0008 ;
>         dicom_0x0008:el_0x0018 = 
> "1.3.12.2.1107.5.1.4.11020.30000015112009095703100004143" ;
>         dicom_0x0008:el_0x1090 = "SOMATOM Definition AS_mCT " ;
>         dicom_0x0008:el_0x0021 = "20151105" ;
>         dicom_0x0008:vartype = "group________" ;
>         dicom_0x0008:el_0x0000 = 856 ;
>         dicom_0x0008:el_0x1010 = "CTAWP71108" ;
>         dicom_0x0008:el_0x0030 = "135819.250000 " ;
>         dicom_0x0008:el_0x1030 = "PET^PETCT_Brain_LM_DIPRE (Adult)" ;
>         dicom_0x0008:el_0x0031 = "143111.000000 " ;
>         dicom_0x0008:el_0x0020 = "20151105" ;
>         dicom_0x0008:el_0x103e = "DIPRE_DYN_UHD_12_21_Z3_256" ;
>         dicom_0x0008:el_0x0080 = "CERMEP" ;
>         dicom_0x0008:el_0x0022 = "20151105" ;
>         dicom_0x0008:el_0x0060 = "PT" ;
>         dicom_0x0008:el_0x0016 = "1.2.840.10008.5.1.4.1.1.128" ;
>         dicom_0x0008:el_0x0070 = "SIEMENS " ;
>         dicom_0x0008:varid = "MNI DICOM variable" ;
>         dicom_0x0008:el_0x1250 = -2b, -1b, 0b, -32b, 38b, 1b, 0b, 0b, 
> 32b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, -128b, 0b, 0b, 0b, 32b, 0b, 13b, 0b, 
> 56b, 0b, 0b, 0b, 49b, 46b, 51b, 46b, 49b, 50b, 46b, 50b, 46b, 49b, 
> 49b, 48b, 55b, 46b, 53b, 46b, 49b, 46b, 52b, 46b, 49b, 49b, 48b, 50b, 
> 48b, 46b, 51b, 48b, 48b, 48b, 48b, 48b, 49b, 53b, 49b, 49b, 48b, 53b, 
> 48b, 55b, 51b, 55b, 48b, 56b, 48b, 57b, 51b, 48b, 48b, 48b, 48b, 48b, 
> 48b, 48b, 57b, 0b, 32b, 0b, 14b, 0b, 56b, 0b, 0b, 0b, 49b, 46b, 51b, 
> 46b, 49b, 50b, 46b, 50b, 46b, 49b, 49b, 48b, 55b, 46b, 53b, 46b, 49b, 
> 46b, 52b, 46b, 49b, 49b, 48b, 50b, 48b, 46b, 51b, 48b, 48b, 48b, 48b, 
> 48b, 49b, 53b, 49b, 49b, 49b, 57b, 48b, 56b, 50b, 55b, 51b, 51b, 51b, 
> 49b, 50b, 48b, 48b, 48b, 49b, 48b, 49b, 55b, 50b, 0b, 64b, 0b, 0b, 0b, 
> 4b, 0b, 0b, 0b, -114b, 0b, 0b, 0b, 64b, 0b, 112b, -95b, -122b, 0b, 0b, 
> 0b, -2b, -1b, 0b, -32b, 126b, 0b, 0b, 0b, 8b, 0b, 0b, 0b, 4b, 0b, 0b, 
> 0b, 114b, 0b, 0b, 0b, 8b, 0b, 0b, 1b, 6b, 0b, 0b, 0b, 49b, 50b, 50b, 
> 52b, 48b, 51b, 8b, 0b, 2b, 1b, 4b, 0b, 0b, 0b, 68b, 67b, 77b, 32b, 8b, 
> 0b, 4b, 1b, 26b, 0b, 0b, 0b, 70b, 111b, 114b, 32b, 65b, 116b, 116b, 
> 101b, 110b, 117b, 97b, 116b, 105b, 111b, 110b, 32b, 67b, 111b, 114b, 
> 114b, 101b, 99b, 116b, 105b, 111b, 110b, 8b, 0b, 5b, 1b, 4b, 0b, 0b, 
> 0b, 68b, 67b, 77b, 82b, 8b, 0b, 6b, 1b, 22b, 0b, 0b, 0b, 50b, 48b, 
> 48b, 51b, 48b, 54b, 49b, 57b, 48b, 48b, 48b, 48b, 48b, 48b, 46b, 48b, 
> 48b, 48b, 48b, 48b, 48b, 32b, 8b, 0b, 15b, 1b, 4b, 0b, 0b, 0b, 55b, 
> 50b, 49b, 48b ;
>         dicom_0x0008:el_0x0008 = "ORIGINAL\\PRIMARY" ;
>         dicom_0x0008:el_0x0005 = "ISO_IR 100" ;
>         dicom_0x0008:el_0x0023 = "20151120" ;
>         dicom_0x0008:el_0x0081 = "Bron Cedex /B7913E/ 69677 Boulevard 
> Pinel 59" ;
>         dicom_0x0008:el_0x1040 = "Department" ;
>         dicom_0x0008:el_0x0032 = "143111.000004 " ;
>         dicom_0x0008:el_0x0033 = "132439.593000 " ;
>     int dicom_0x0010 ;
>         dicom_0x0010:el_0x0010 = "BENSU06591" ;
>         dicom_0x0010:vartype = "group________" ;
>         dicom_0x0010:el_0x0000 = 100 ;
>         dicom_0x0010:el_0x1010 = "023Y" ;
>         dicom_0x0010:el_0x0030 = "19920101" ;
>         dicom_0x0010:el_0x1030 = "54" ;
>         dicom_0x0010:el_0x0040 = "F " ;
>         dicom_0x0010:el_0x0020 = "BENSU ESTOUR DPN SPORTIFS " ;
>         dicom_0x0010:varid = "MNI DICOM variable" ;
>     int dicom_0x0018 ;
>         dicom_0x0018:el_0x1020 = "syngo MI.PET/CT 2012A " ;
>         dicom_0x0018:vartype = "group________" ;
>         dicom_0x0018:el_0x5100 = "HFS " ;
>         dicom_0x0018:el_0x1181 = "NONE" ;
>         dicom_0x0018:el_0x1210 = "All-pass" ;
>         dicom_0x0018:el_0x1000 = "11020 " ;
>         dicom_0x0018:el_0x0000 = 174 ;
>         dicom_0x0018:el_0x1242 = "20000 " ;
>         dicom_0x0018:el_0x1201 = "081350.000000\\141756.000000 " ;
>         dicom_0x0018:el_0x0050 = "2.027 " ;
>         dicom_0x0018:varid = "MNI DICOM variable" ;
>         dicom_0x0018:el_0x1200 = "20151105\\20150601 " ;
>     int dicom_0x0020 ;
>         dicom_0x0020:el_0x4000 = "AC CT Brain, Volume Scaled" ;
>         dicom_0x0020:el_0x0010 = "1 " ;
>         dicom_0x0020:vartype = "group________" ;
>         dicom_0x0020:el_0x000d = 
> "1.3.12.2.1107.5.1.4.11020.30000015110507370809300000009" ;
>         dicom_0x0020:el_0x0000 = 356 ;
>         dicom_0x0020:el_0x0012 = "2001" ;
>         dicom_0x0020:el_0x1041 = "-439.729" ;
>         dicom_0x0020:el_0x1001 = "0 " ;
>         dicom_0x0020:el_0x0013 = "1 " ;
>         dicom_0x0020:el_0x000e = 
> "1.3.12.2.1107.5.1.4.11020.30000015112009095703100008067" ;
>         dicom_0x0020:el_0x0011 = "7 " ;
>         dicom_0x0020:varid = "MNI DICOM variable" ;
>         dicom_0x0020:el_0x0052 = 
> "1.3.12.2.1107.5.1.4.11020.30000015110507371409300000019" ;
>         dicom_0x0020:el_0x0032 = "-136.82\\-371.453\\-439.729 " ;
>         dicom_0x0020:el_0x0037 = "1\\0\\0\\0\\1\\0 " ;
>     int dicom_0x0021 ;
>         dicom_0x0021:vartype = "group________" ;
>         dicom_0x0021:el_0x0000 = 30 ;
>         dicom_0x0021:el_0x1370 = "0 " ;
>         dicom_0x0021:el_0x1330 = "1 " ;
>         dicom_0x0021:varid = "MNI DICOM variable" ;
>         dicom_0x0021:el_0x1340 = "0 " ;
>     int dicom_0x0023 ;
>         dicom_0x0023:vartype = "group________" ;
>         dicom_0x0023:el_0x0000 = 24 ;
>         dicom_0x0023:el_0x0006 = "\ufffdYt\ufffd\ufffd" ;
>         dicom_0x0023:varid = "MNI DICOM variable" ;
>         dicom_0x0023:el_0x0008 = "0 " ;
>     int dicom_0x0028 ;
>         dicom_0x0028:el_0x0010 = 256s ;
>         dicom_0x0028:vartype = "group________" ;
>         dicom_0x0028:el_0x0004 = "MONOCHROME2 " ;
>         dicom_0x0028:el_0x0103 = 0s ;
>         dicom_0x0028:el_0x0000 = 236 ;
>         dicom_0x0028:el_0x1054 = "BQML" ;
>         dicom_0x0028:el_0x0100 = 16s ;
>         dicom_0x0028:el_0x0102 = 15b, 0b ;
>         dicom_0x0028:el_0x0030 = "1.06063\\1.06063 " ;
>         dicom_0x0028:el_0x1053 = "34.968733588672 " ;
>         dicom_0x0028:el_0x0107 = 0b, 0b ;
>         dicom_0x0028:el_0x0106 = 0b, 0b ;
>         dicom_0x0028:el_0x0051 = "NORM\\DTIM\\ATTN\\SCAT\\DECY\\RAN" ;
>         dicom_0x0028:el_0x1052 = "0 " ;
>         dicom_0x0028:el_0x0011 = 256s ;
>         dicom_0x0028:varid = "MNI DICOM variable" ;
>         dicom_0x0028:el_0x0101 = 16s ;
>         dicom_0x0028:el_0x1050 = "0 " ;
>         dicom_0x0028:el_0x1051 = "1 " ;
>         dicom_0x0028:el_0x0002 = 1b, 0b ;
>     int dicom_0x0029 ;
>         dicom_0x0029:el_0x0010 = "SIEMENS CSA HEADER" ;
>         dicom_0x0029:el_0x1020 = 
> "<pds><com>gm:1104,236,0,0,go:-1.059,0.308,754.271,0.042,0.038,0.001,QC:1,1,0,101.8,39.6,31.7,0,1,0,0.2,0.8,0,3.109e+007,zo:3,xO:0,yO:0,CT:1.3.12.2.1107.5.1.4.11020.30000015111908273331200010172</com><dat><fg>1.3.12.2.1107.5.1.4.11020.30000015110508273160900000065,DFDef:0,0,20-1,20,40-2,40,60-3,60,80-4,80,100-5,100,120-6,120,140-7,140,160-8,160,180-9,180,200-10,200,220-11,220,240-12,240,260-13,260,280-14,280,300-15,300,420-16,420,540-17,540,660-18,660,780-19,780,900-20,900,1020-21,1020,1140-22,1140,1260-23,1260,1380-24,1380,1500-25,1500,1620-26,1620,1740-27,1740,1860-28,1860,1980-29,1980,2100-30,2100,2400-31,2400,2700-32,2700,3000-33,3000,3300-34,3300,3600-35,3600,3900-36,3900,4200-</fg></dat></pds>\r\n",
>             "" ;
>         dicom_0x0029:vartype = "group________" ;
>         dicom_0x0029:el_0x0000 = 780 ;
>         dicom_0x0029:varid = "MNI DICOM variable" ;
>         dicom_0x0029:el_0x1018 = "PET_REPLAY_PARAM" ;
>         dicom_0x0029:el_0x1019 = "1.3 " ;
>     int dicom_0x0054 ;
>         dicom_0x0054:el_0x0410 = -2b, -1b, 0b, -32b, -8b, 0b, 0b, 0b, 
> 8b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, 100b, 0b, 0b, 0b, 8b, 0b, 0b, 1b, 8b, 
> 0b, 0b, 0b, 70b, 45b, 49b, 48b, 52b, 53b, 48b, 32b, 8b, 0b, 2b, 1b, 
> 6b, 0b, 0b, 0b, 57b, 57b, 83b, 68b, 77b, 32b, 8b, 0b, 4b, 1b, 10b, 0b, 
> 0b, 0b, 114b, 101b, 99b, 117b, 109b, 98b, 101b, 110b, 116b, 32b, 8b, 
> 0b, 5b, 1b, 4b, 0b, 0b, 0b, 68b, 67b, 77b, 82b, 8b, 0b, 6b, 1b, 22b, 
> 0b, 0b, 0b, 50b, 48b, 48b, 50b, 48b, 57b, 48b, 52b, 48b, 48b, 48b, 
> 48b, 48b, 48b, 46b, 48b, 48b, 48b, 48b, 48b, 48b, 32b, 8b, 0b, 15b, 
> 1b, 2b, 0b, 0b, 0b, 49b, 57b, 84b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, 124b, 
> 0b, 0b, 0b, 84b, 0b, 18b, 4b, 116b, 0b, 0b, 0b, -2b, -1b, 0b, -32b, 
> 108b, 0b, 0b, 0b, 8b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, 96b, 0b, 0b, 0b, 8b, 
> 0b, 0b, 1b, 8b, 0b, 0b, 0b, 70b, 45b, 49b, 48b, 51b, 52b, 48b, 32b, 
> 8b, 0b, 2b, 1b, 6b, 0b, 0b, 0b, 57b, 57b, 83b, 68b, 77b, 32b, 8b, 0b, 
> 4b, 1b, 6b, 0b, 0b, 0b, 115b, 117b, 112b, 105b, 110b, 101b, 8b, 0b, 
> 5b, 1b, 4b, 0b, 0b, 0b, 68b, 67b, 77b, 82b, 8b, 0b, 6b, 1b, 22b, 0b, 
> 0b, 0b, 50b, 48b, 48b, 50b, 48b, 57b, 48b, 52b, 48b, 48b, 48b, 48b, 
> 48b, 48b, 46b, 48b, 48b, 48b, 48b, 48b, 48b, 32b, 8b, 0b, 15b, 1b, 2b, 
> 0b, 0b, 0b, 50b, 48b ;
>         dicom_0x0054:el_0x1105 = "Model-based " ;
>         dicom_0x0054:el_0x1300 = "9990.5540141915 " ;
>         dicom_0x0054:vartype = "group________" ;
>         dicom_0x0054:el_0x0414 = -2b, -1b, 0b, -32b, 112b, 0b, 0b, 0b, 
> 8b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, 100b, 0b, 0b, 0b, 8b, 0b, 0b, 1b, 8b, 
> 0b, 0b, 0b, 70b, 45b, 49b, 48b, 52b, 55b, 48b, 32b, 8b, 0b, 2b, 1b, 
> 6b, 0b, 0b, 0b, 57b, 57b, 83b, 68b, 77b, 32b, 8b, 0b, 4b, 1b, 10b, 0b, 
> 0b, 0b, 104b, 101b, 97b, 100b, 102b, 105b, 114b, 115b, 116b, 32b, 8b, 
> 0b, 5b, 1b, 4b, 0b, 0b, 0b, 68b, 67b, 77b, 82b, 8b, 0b, 6b, 1b, 22b, 
> 0b, 0b, 0b, 50b, 48b, 48b, 50b, 48b, 57b, 48b, 52b, 48b, 48b, 48b, 
> 48b, 48b, 48b, 46b, 48b, 48b, 48b, 48b, 48b, 48b, 32b, 8b, 0b, 15b, 
> 1b, 2b, 0b, 0b, 0b, 50b, 49b ;
>         dicom_0x0054:el_0x1101 = "measured,AC CT Brain" ;
>         dicom_0x0054:el_0x1000 = "DYNAMIC\\IMAGE " ;
>         dicom_0x0054:el_0x1322 = "31086800" ;
>         dicom_0x0054:el_0x1102 = "START " ;
>         dicom_0x0054:el_0x0000 = 964 ;
>         dicom_0x0054:el_0x1100 = "DLYD" ;
>         dicom_0x0054:el_0x1321 = "1.00568 " ;
>         dicom_0x0054:el_0x1001 = "BQML" ;
>         dicom_0x0054:el_0x1201 = "5\\6 " ;
>         dicom_0x0054:el_0x0013 = -2b, -1b, 0b, -32b, 36b, 0b, 0b, 0b, 
> 84b, 0b, 0b, 0b, 4b, 0b, 0b, 0b, 24b, 0b, 0b, 0b, 84b, 0b, 20b, 0b, 
> 4b, 0b, 0b, 0b, 52b, 51b, 53b, 32b, 84b, 0b, 21b, 0b, 4b, 0b, 0b, 0b, 
> 54b, 53b, 48b, 32b ;
>         dicom_0x0054:el_0x0016 = 
> "\ufffd\ufffd\ufffd\ufffdN1\bSolutionr143000.000000 t\n",
>             "177380000 u1223v1 
> T\ufffdTx\ufffd\ufffd\ufffdp\bd\b\bC-105A1 \bSRT \b\n",
>             "^11^Carbon\bDCMR\b20070625000000.000000 \b4020" ;
>         dicom_0x0054:el_0x1330 = 1s ;
>         dicom_0x0054:varid = "MNI DICOM variable" ;
>         dicom_0x0054:el_0x1323 = "0.322837" ;
>         dicom_0x0054:el_0x0081 = 109s ;
>         dicom_0x0054:el_0x1002 = "EMISSION" ;
>         dicom_0x0054:el_0x0101 = 37s ;
>         dicom_0x0054:el_0x1200 = "49" ;
>         dicom_0x0054:el_0x1103 = "PSF+TOF 12i21s" ;
>     int dicom_0x0071 ;
>         dicom_0x0071:el_0x0010 = "SIEMENS MED PT" ;
>         dicom_0x0071:vartype = "group________" ;
>         dicom_0x0071:el_0x0000 = 52 ;
>         dicom_0x0071:el_0x1022 = "20151105143111.000000 " ;
>         dicom_0x0071:varid = "MNI DICOM variable" ;
>     int dicom_groups ;
>         dicom_groups:vartype = "group________" ;
>         dicom_groups:varid = "MNI DICOM variable" ;
>     int dicominfo ;
>         dicominfo:vartype = "group________" ;
>         dicominfo:window_min = -0.5 ;
>         dicominfo:varid = "MNI DICOM information variable" ;
>         dicominfo:window_max = 1145820. ;
>         dicominfo:image_type = "ORIGINAL\\PRIMARY" ;
>     int patient ;
>         patient:version = "MINC Version    1.0" ;
>         patient:full_name = "BENSU06591" ;
>         patient:vartype = "group________" ;
>         patient:age = 23. ;
>         patient:weight = 54. ;
>         patient:birthdate = "19920101" ;
>         patient:position = "HFS " ;
>         patient:sex = "female" ;
>         patient:identification = "BENSU ESTOUR DPN SPORTIFS " ;
>         patient:varid = "MINC standard variable" ;
>     int study ;
>         study:serial_no = "11020 " ;
>         study:procedure = "PET^PETCT_Brain_LM_DIPRE (Adult)" ;
>         study:station_id = "CTAWP71108" ;
>         study:study_id = "20151104.135819" ;
>         study:software_version = "syngo MI.PET/CT 2012A " ;
>         study:version = "MINC Version    1.0" ;
>         study:vartype = "group________" ;
>         study:calibration_time = "081350.000000\\141756.000000 " ;
>         study:institution = "CERMEP" ;
>         study:modality = "PET__" ;
>         study:start_date = "20151105" ;
>         study:device_model = "SOMATOM Definition AS_mCT " ;
>         study:varid = "MINC standard variable" ;
>         study:calibration_date = "20151105\\20150601 " ;
>         study:manufacturer = "SIEMENS " ;
>         study:start_time = "135819.250000 " ;
>
> // global attributes:
>         :ident = "redoute:apollon:2017.06.07.16.34.56:19987:1" ;
>         :minc_version = "2.4.02" ;
>         :history = "Wed Jun  7 16:29:42 2017>>> dcm2mnc 
> -adjust_frame_time -dname  -fname BENSU_DPN_DYN_37F 
> /home/chuste/SPORTIVES_DPN/DICOM/BENSU/BENSU_DPN_DYN ./\n",
>             "Wed Jun  7 16:29:56 2017>>> mincreshape +xdirection 
> +ydirection +zdirection BENSU_DPN_DYN_37F.mnc TMP.mnc\n",
>             "Wed Jun  7 16:34:56 2017>>> mincaverage -avgdim time 
> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F.mnc 
> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F_sum.mnc\n",
>             "" ;
> data:
>
>  image-min = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
> 0, 0,
>     0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
> 0, 0,
>     0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
> 0, 0,
>     0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
> 0, 0,
>     0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ;
>
>  image-max = 1015.97951002534, 1240.91749194396, 630.382305503898,
>     723.002194468489, 511.299591120853, 450.813133021528, 
> 410.170996250848,
>     336.455923177493, 332.677163576246, 350.630994662977, 
> 544.378295949706,
>     338.345692353633, 487.672068425804, 521.697085552957, 
> 431.911158129436,
>     770.256821640438, 2799.38299059135, 7770.62034174942, 
> 8482.28947336752,
>     7311.29238818473, 8237.5266244748, 8216.71158998212, 
> 7388.81507791155,
>     6908.67382041203, 6631.77800213614, 13994.1722639211, 
> 25789.0164509082,
>     23597.3480681966, 22800.5333269836, 27038.4614541529, 
> 24876.0739949538,
>     23241.9655096776, 23723.9253238975, 23875.1954337083, 
> 23959.2471432625,
>     25403.3672287019, 26914.6309831411, 26450.5532251209, 
> 26689.7233004063,
>     28028.9090779358, 27474.0787172964, 24943.1621707318, 
> 26341.8762397411,
>     27439.9909818683, 28157.3802273092, 28828.315531433, 
> 27267.0795538751,
>     27136.666213844, 27628.9816285747, 26338.0979560432, 
> 25649.1439537558,
>     24497.976667637, 25563.0949208548, 31710.9625537502, 
> 28759.5265633965,
>     29021.1731529272, 26897.6213588406, 26410.8196023807, 
> 29460.6965591512,
>     28964.4353283011, 27777.4142003581, 28767.9773100351, 26587.64885472,
>     28103.502048587, 26836.0683435148, 25409.0242348483, 
> 26819.1750127021,
>     25862.6754683284, 27790.6644761479, 26720.8615018712, 
> 29452.1399744785,
>     86457.7847388781, 96697.9745770936, 27089.5121032407, 
> 26246.2997936328,
>     26895.6974255682, 28537.3314435693, 24599.9965574869, 
> 27394.7222563613,
>     27130.0692263568, 22924.2698431253, 21530.3207497954, 
> 14907.0967220738,
>     16521.2481834412, 16741.6011532759, 16129.122218676, 
> 14679.4045717525,
>     17194.2099996542, 15261.4439887782, 15532.7040867694, 
> 16324.6789335692,
>     12881.7204989359, 10639.9370643974, 11762.7352867794, 
> 11214.4996639019,
>     12202.2473434282, 11111.5606026694, 15651.7596746581, 
> 13704.0686550507,
>     13669.0525041769, 16991.0475695223, 16069.6059257307, 
> 15393.7603655957,
>     16025.2247745041, 15350.2913481498, 21429.1910733267, 
> 25955.3927300149,
>     36845.5970575126, 37132.9700624098 ;
>
>  xspace = 0 ;
>
>  yspace = 0 ;
>
>  zspace = 0 ;
>
>  acquisition = 0 ;
>
>  dicom_0x0008 = 0 ;
>
>  dicom_0x0010 = 0 ;
>
>  dicom_0x0018 = 0 ;
>
>  dicom_0x0020 = 0 ;
>
>  dicom_0x0021 = 0 ;
>
>  dicom_0x0023 = 0 ;
>
>  dicom_0x0028 = 0 ;
>
>  dicom_0x0029 = 0 ;
>
>  dicom_0x0054 = 0 ;
>
>  dicom_0x0071 = 0 ;
>
>  dicom_groups = 0 ;
>
>  dicominfo = 0 ;
>
>  patient = 0 ;
>
>  study = 0 ;
> }



Le 07/06/2017 ? 17:08, Robert D. Vincent a ?crit :
> Hi Jerome,
>
> I'm not sure. Those warnings may not be telling us anything important. Does
> the output of mincresample look good?
>
> Can you send the output of mincheader for TEP_sum.mnc?
>
>      -bert
>
> On Wed, Jun 7, 2017 at 10:51 AM, J?r?me Redout? <redoute at cermep.fr> wrote:
>
>> Hi all,
>>
>> here is the problem we are facing with:
>>
>> 1. dcm2mnc DICOM to TEP_DYN.mnc
>>
>> 2. mincaverage  -avgdim time TEP_DYN.mnc TEP_sum.mnc
>>
>> 3. mnc2nii TEP_sum.mnc TEP_sum.nii
>>
>> 3. we use SPM to coregister TEP_sum.nii with MRI, segment MRI and then
>> push ATLAS.nii in TEP_sum space
>>
>> 4. at this point: ATLAS.nii and TEP_sum.nii are well coregistred when
>> checking with register
>>
>> 5. nii2mnc -byte ATLAS.nii ATLAS.mnc
>>
>> 6. then we need to resample ATLAS.mnc:
>>
>>      mincresample -verbose -nearest_neighbour -byte -like TEP_sum.mnc
>> ATLAS.mnc ATLAS_Res.mnc
>>
>> the problem is at this step:
>>
>> we get warnings:
>>
>> WARN: Irregular dimension in file TEP_sum.mnc contains non-monotonic or
>>> repeated values.
>>> WARN: Something is wrong with the irregular dimension in file TEP_sum.mnc.
>>>        Substituting a step size of 1.0.
>>> WARN: Irregular dimension in file EP_sum.mnc contains non-monotonic or
>>> repeated values.
>>> WARN: Something is wrong with the irregular dimension in file EP_sum.mnc.
>>>        Substituting a step size of 1.0.
>>> WARN: Irregular dimension in file EP_sum.mnc contains non-monotonic or
>>> repeated values.
>>> WARN: Something is wrong with the irregular dimension in file EP_sum.mnc.
>>>        Substituting a step size of 1.0.
>>>
>> and the resulting ATLAS_Res.mnc is not coregistred with TEP_sum.mnc
>>
>> Any ideas n what is wrong with our reference image?
>>
>> thank you
>>
>> Jerome
>>
>>
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From bert at phalarope.com  Wed Jun  7 12:10:28 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Wed, 7 Jun 2017 12:10:28 -0400
Subject: [MINC-users] mincresample -like problem
In-Reply-To: <180b98fd-4719-5a76-3f7d-6495f124dd12@cermep.fr>
References: <58c61418-f37f-bdff-af90-d8b7f67860be@cermep.fr>
	<CAAd5DeT-bgNZF4F9RwjFbwJYhf0v2wex3ZqBb33Zqsj=Ep7dPQ@mail.gmail.com>
	<180b98fd-4719-5a76-3f7d-6495f124dd12@cermep.fr>
Message-ID: <CAAd5DeQPa2t7ojJhD3CUVOt0ieA6KdM+0j==teMAY7+kYoDTsw@mail.gmail.com>

HI Jerome,

The version of mincaverage you are using is creating a strange, possibly
incorrect output file.

Please try the following with the output of mincaverage:

minc_modify_header -sinsert zspace:spacing=regular infile.mnc outfile.mnc

and use the output of this command as the input to the -like option of
mincresample.

    -bert

From redoute at cermep.fr  Thu Jun  8 08:17:22 2017
From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=)
Date: Thu, 8 Jun 2017 14:17:22 +0200
Subject: [MINC-users] mincresample -like problem
In-Reply-To: <CAAd5DeQPa2t7ojJhD3CUVOt0ieA6KdM+0j==teMAY7+kYoDTsw@mail.gmail.com>
References: <58c61418-f37f-bdff-af90-d8b7f67860be@cermep.fr>
	<CAAd5DeT-bgNZF4F9RwjFbwJYhf0v2wex3ZqBb33Zqsj=Ep7dPQ@mail.gmail.com>
	<180b98fd-4719-5a76-3f7d-6495f124dd12@cermep.fr>
	<CAAd5DeQPa2t7ojJhD3CUVOt0ieA6KdM+0j==teMAY7+kYoDTsw@mail.gmail.com>
Message-ID: <9b109730-bf97-7510-b81f-6dcccab20b6a@cermep.fr>

Hi,
Thank you Robert,

this seems to fix the problem, but I had to also modify yspace and 
xspace in the same way because these WARN subsisted:

> WARN: Irregular dimension in file 
> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F_sum.mnc 
> contains non-monotonic or repeated values.
> WARN: Something is wrong with the irregular dimension in file 
> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F_sum.mnc.
>       Substituting a step size of 1.0.
> WARN: Irregular dimension in file 
> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F_sum.mnc 
> contains non-monotonic or repeated values.
> WARN: Something is wrong with the irregular dimension in file 
> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F_sum.mnc.
>       Substituting a step size of 1.0.


few questions then:

the problem is also present in the PET_DYN.mnc that comes from dcm2mnc 
conversion (can't use it for the -like option)

do I need to also correct the DYN file ?
What are the consequences of such a correction? (don't know exactly what 
is the meaning of this "regular" option...

Thank you again for your precious help

Jerome





Le 07/06/2017 ? 18:10, Robert D. Vincent a ?crit :
> HI Jerome,
>
> The version of mincaverage you are using is creating a strange, possibly
> incorrect output file.
>
> Please try the following with the output of mincaverage:
>
> minc_modify_header -sinsert zspace:spacing=regular infile.mnc outfile.mnc
>
> and use the output of this command as the input to the -like option of
> mincresample.
>
>      -bert
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


-- 
==================================================================
J?r?me Redout?
Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1
CERMEP - Imagerie du vivant
59 Bd Pinel. 69677 Bron - FRANCE
tel : 33 (0)4 72 68 86 18 (bureau)
tel : 33 (0)4 72 68 86 00 (standard)
fax : 33 (0)4 72 68 86 10
==================================================================



From bert at phalarope.com  Thu Jun  8 08:50:59 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Thu, 8 Jun 2017 08:50:59 -0400
Subject: [MINC-users] mincresample -like problem
In-Reply-To: <9b109730-bf97-7510-b81f-6dcccab20b6a@cermep.fr>
References: <58c61418-f37f-bdff-af90-d8b7f67860be@cermep.fr>
	<CAAd5DeT-bgNZF4F9RwjFbwJYhf0v2wex3ZqBb33Zqsj=Ep7dPQ@mail.gmail.com>
	<180b98fd-4719-5a76-3f7d-6495f124dd12@cermep.fr>
	<CAAd5DeQPa2t7ojJhD3CUVOt0ieA6KdM+0j==teMAY7+kYoDTsw@mail.gmail.com>
	<9b109730-bf97-7510-b81f-6dcccab20b6a@cermep.fr>
Message-ID: <CAAd5DeR3LiZ-jz=-a6zLGwY1GUQ7BuxDw=6ZRmsL-Gj2ve0QKw@mail.gmail.com>

Hi Jerome,

Irregular dimensions in MINC are used to represent situations like a PET
acquisition with irregularly-spaced sample points in time. Irregular
dimensions are represented with a vector of sample points, in some places
the code checks that the sample points are valid (monotonically increasing,
with no repeated values). We should see errors only if there is something
wrong with the original DICOM.

Most spatial dimensions in MRI and PET are regular, meaning that they can
be expressed with just a pair of values that represent a start and step.

In the file header you sent, the spatial dimensions are marked as
irregular, but they have the correct attributes to be treated as regular.

     -bert

On Thu, Jun 8, 2017 at 8:17 AM, J?r?me Redout? <redoute at cermep.fr> wrote:

> Hi,
> Thank you Robert,
>
> this seems to fix the problem, but I had to also modify yspace and xspace
> in the same way because these WARN subsisted:
>
> WARN: Irregular dimension in file /home/redoute/protocoles/TEP/S
>> PORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F_sum.mnc contains non-monotonic or
>> repeated values.
>> WARN: Something is wrong with the irregular dimension in file
>> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_
>> DYN_37F_sum.mnc.
>>       Substituting a step size of 1.0.
>> WARN: Irregular dimension in file /home/redoute/protocoles/TEP/S
>> PORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F_sum.mnc contains non-monotonic or
>> repeated values.
>> WARN: Something is wrong with the irregular dimension in file
>> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_
>> DYN_37F_sum.mnc.
>>       Substituting a step size of 1.0.
>>
>
>
> few questions then:
>
> the problem is also present in the PET_DYN.mnc that comes from dcm2mnc
> conversion (can't use it for the -like option)
>
> do I need to also correct the DYN file ?
> What are the consequences of such a correction? (don't know exactly what
> is the meaning of this "regular" option...
>
> Thank you again for your precious help
>
> Jerome
>
>
>
>
>
>
> Le 07/06/2017 ? 18:10, Robert D. Vincent a ?crit :
>
>> HI Jerome,
>>
>> The version of mincaverage you are using is creating a strange, possibly
>> incorrect output file.
>>
>> Please try the following with the output of mincaverage:
>>
>> minc_modify_header -sinsert zspace:spacing=regular infile.mnc outfile.mnc
>>
>> and use the output of this command as the input to the -like option of
>> mincresample.
>>
>>      -bert
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
> --
> ==================================================================
> J?r?me Redout?
> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1
> CERMEP - Imagerie du vivant
> 59 Bd Pinel. 69677 Bron - FRANCE
> tel : 33 (0)4 72 68 86 18 (bureau)
> tel : 33 (0)4 72 68 86 00 (standard)
> fax : 33 (0)4 72 68 86 10
> ==================================================================
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From andrew at biospective.com  Thu Jun  8 15:00:33 2017
From: andrew at biospective.com (Andrew Wood)
Date: Thu, 8 Jun 2017 15:00:33 -0400
Subject: [MINC-users] Intensity Profile in Display
Message-ID: <CABApf9HnfYpzL+d09=FAyZ8yks1b2eBNoFVM7D-c1VhYJhvsUA@mail.gmail.com>

Hi all,

Is there is a Display.globals variable that can disable the intensity
profile curve in the bottom-right panel of the slice view window?

Thanks,
Andrew

From bert at phalarope.com  Thu Jun  8 15:28:16 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Thu, 8 Jun 2017 15:28:16 -0400
Subject: [MINC-users] Intensity Profile in Display
In-Reply-To: <CABApf9HnfYpzL+d09=FAyZ8yks1b2eBNoFVM7D-c1VhYJhvsUA@mail.gmail.com>
References: <CABApf9HnfYpzL+d09=FAyZ8yks1b2eBNoFVM7D-c1VhYJhvsUA@mail.gmail.com>
Message-ID: <CAAd5DeRu2Y0UCyKrCGRhyD8YzNcge-Ef8CtCXLe04EYnkpfc3Q@mail.gmail.com>

There's no global to disable it at the moment, it can only be disabled from
the menu.

    -bert

On Thu, Jun 8, 2017 at 3:00 PM, Andrew Wood <andrew at biospective.com> wrote:

> Hi all,
>
> Is there is a Display.globals variable that can disable the intensity
> profile curve in the bottom-right panel of the slice view window?
>
> Thanks,
> Andrew
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From stebollmann at gmail.com  Fri Jun  9 21:42:48 2017
From: stebollmann at gmail.com (Steffen Bollmann)
Date: Sat, 10 Jun 2017 11:42:48 +1000
Subject: [MINC-users] undefined reference to `jpeg_mem_src'
In-Reply-To: <CAAd5DeTidK1h42wu6BWX2nw+hSfkvkoXz8ErdvgNSKEb98LDbg@mail.gmail.com>
References: <CAEimUjiopLKOoZXsxaZ-mOpEAwHVYYdzc+VEti+V-nQq0M=eUw@mail.gmail.com>
	<CAAd5DeTidK1h42wu6BWX2nw+hSfkvkoXz8ErdvgNSKEb98LDbg@mail.gmail.com>
Message-ID: <CAEimUjigRbVkpbVtQSwWWtCDup384rWqXVV7U6y78xbaE8vZqA@mail.gmail.com>

Dear Robert,

Thank you for your help. The problem was indeed the libjpeg version, but I
had some trouble updating it, because I tried compiling minc on our cluster
running on 2.6.32-573.18.1.el6.x86_64 and the most recent version of
libjpeg from the module system was still too old.

In case anyone else has that problem, here is how I solved it: (I had to do
a few more things, since the installed cmake on the cluster was not
compiled with https support and it failed downloading many of the minc
packages, also NASM wasn't available)

Fix curl

git clone https://github.com/curl/curl.git

cd curl

./buildconf

./configure --prefix=/RDS/Q0306/sw/curl

make -j4

make install


add /RDS/Q0306/sw/curl/bin to PATH



Fix cmake

wget https://cmake.org/files/v3.9/cmake-3.9.0-rc1.tar.gz

tar -xf cmake-3.9.0-rc1.tar.gz

cd  cmake-3.9.0-rc1

./bootstrap --system-curl --prefix=/RDS/Q0306/sw/cmake

make -j4

make install



add /RDS/Q0306/sw/cmake/bin to PATH





Fix NASM

git clone https://github.com/letolabs/nasm

cd nasm

./autogen.sh

sh configure --prefix=/RDS/Q0306/sw/nasm

make -j4

make install



add /Q0306/sw/nasm/bin to PATH





Compile MINC-toolkit-v2

git clone -b develop --recursive
https://github.com/BIC-MNI/minc-toolkit-v2.git minc-toolkit-v2-2017-05-25/



cd minc-toolkit-v2-2017-05-25/



mkdir build && cd build





Fix Libjpeg:

git clone https://github.com/libjpeg-turbo/libjpeg-turbo

autoreconf -fiv

sh configure --prefix=/RDS/Q0306/sw/libjpeg-turbo

make install



TO MAKE IT USE THE LIBJPEG REPLACE THE PATHS IN
minc-toolkit-v2-2017-05-25/minctools/conversion/CMakeLists.txt



TARGET_LINK_LIBRARIES(/RDS/Q0306/sw/libjpeg-turbo/lib/libjpeg.so)

INCLUDE_DIRECTORIES(/RDS/Q0306/sw/libjpeg-turbo/include)

TARGET_LINK_LIBRARIES(dcm2mnc /RDS/Q0306/sw/libjpeg-turbo/lib/libjpeg.so)



cmake .. \
-DCMAKE_BUILD_TYPE:STRING=Release   \
-DCMAKE_INSTALL_PREFIX:PATH=/RDS/Q0306/sw/minc-itk4-2017-06-10-flashlite-el6/
\
-DMT_BUILD_ABC:BOOL=ON   \
-DMT_BUILD_ANTS:BOOL=ON   \
-DMT_BUILD_C3D:BOOL=ON   \
-DMT_BUILD_ELASTIX:BOOL=ON   \
-DMT_BUILD_IM:BOOL=OFF   \
-DMT_BUILD_ITK_TOOLS:BOOL=ON   \
-DMT_BUILD_LITE:BOOL=OFF   \
-DMT_BUILD_SHARED_LIBS:BOOL=ON   \
-DMT_BUILD_VISUAL_TOOLS:BOOL=ON \
-DMT_USE_OPENMP:BOOL=ON   \
-DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
-DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
-DUSE_SYSTEM_GLUT:BOOL=OFF   \
-DUSE_SYSTEM_GSL:BOOL=OFF   \
-DUSE_SYSTEM_HDF5:BOOL=OFF   \
-DUSE_SYSTEM_ITK:BOOL=OFF   \
-DUSE_SYSTEM_NETCDF:BOOL=OFF   \
-DUSE_SYSTEM_NIFTI:BOOL=OFF   \
-DUSE_SYSTEM_PCRE:BOOL=OFF   \
-DUSE_SYSTEM_ZLIB:BOOL=OFF



make -j4



make install



I also had this problem on the way as soon as I tried to use a recent
version of GCC:

[ 85%] Built target ITKIOGIPL-all

/usr/bin/ld: CMakeFiles/ITKIOHDF5.dir/itkHDF5ImageIO.cxx.o: relocation
R_X86_64_PC32 against undefined symbol `H5::DataType::fromClass() const'
can not be used when making a shared object; recompile with -fPIC

/usr/bin/ld: final link failed: Bad value

collect2: ld returned 1 exit status

make[5]: *** [lib/libITKIOHDF5-4.11.so.1] Error 1

make[4]: *** [Modules/IO/HDF5/src/CMakeFiles/ITKIOHDF5.dir/all] Error 2

make[3]: *** [all] Error 2

make[2]: *** [ITKv4-prefix/src/ITKv4-stamp/ITKv4-build] Error 2

make[1]: *** [CMakeFiles/ITKv4.dir/all] Error 2

make: *** [all] Error 2


I could not figure out where to set -fPIC, so I solved it badly by using an
old version of gcc (4.4.7).


Now it all seems to work. Is there anything I could have done better in
solving this issue - I am still learning and input in how to do things
better are very much appreciated. Maybe it helps in making compiling minc
more straight forward and you can change things in the makefiles to account
for these problems and get more people to use it - it is a wonderful
toolkit - just hard to get it working (at least for me).


Thanks for you help

Steffen



2017-05-24 20:16 GMT+10:00 Robert D. Vincent <bert at phalarope.com>:

> You probably need to install a different version of libjpeg-dev
>
> I've been successfully building with libjpeg8-dev installed on a Ubuntu
> 16.04 system.
>
>    -bert
>
> On Wed, May 24, 2017 at 3:28 AM, Steffen Bollmann <stebollmann at gmail.com>
> wrote:
>
> > Hi all,
> >
> > I am trying to compile minc-toolkit-v2 develop and I get this error:
> >
> > [ 44%] Linking C executable dcm2mnc
> > CMakeFiles/dcm2mnc.dir/dcm2mnc/dicom_read.c.o: In function
> > `dicom_jpeg_decompress':
> > dicom_read.c:(.text+0x4a4): undefined reference to `jpeg_mem_src'
> > collect2: ld returned 1 exit status
> > make[2]: *** [minctools/conversion/dcm2mnc] Error 1
> > make[1]: *** [minctools/conversion/CMakeFiles/dcm2mnc.dir/all] Error 2
> > make: *** [all] Error 2
> >
> > How can I find out what is causing that error? Is it a missing library on
> > the system where I build it? Could it be that libjpeg-dev is the culprit
> > (guessing from 'jpeg_mem_src')?
> >
> > Thank you for any hints
> > Steffen
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From raquib.ridwan at gmail.com  Mon Jun 12 16:06:33 2017
From: raquib.ridwan at gmail.com (Raquib Ridwan)
Date: Mon, 12 Jun 2017 15:06:33 -0500
Subject: [MINC-users] Regarding the documentation of volume_pol for
	normalization
Message-ID: <CAGCVZ0=g2+UhrUoV4-iCNi4M3BY1O7SbOaz5abZGFHHXDtVpMg@mail.gmail.com>

Hi,

I would like to know what volume_pol does for normalization. I seem to not
find out any documentation of volume_pol and volume_nuyl

*Sincerely,*
*Abdur Raquib Ridwan, M.Sc *
*PhD student at IIT(Chicago,USA)*
*Research Assistant at MIRC*
*Specialization in MRI imaging*

From vladimir.fonov at gmail.com  Mon Jun 12 16:21:28 2017
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 12 Jun 2017 16:21:28 -0400
Subject: [MINC-users] Regarding the documentation of volume_pol for
	normalization
In-Reply-To: <CAGCVZ0=g2+UhrUoV4-iCNi4M3BY1O7SbOaz5abZGFHHXDtVpMg@mail.gmail.com>
References: <CAGCVZ0=g2+UhrUoV4-iCNi4M3BY1O7SbOaz5abZGFHHXDtVpMg@mail.gmail.com>
Message-ID: <CAMCwi7PuqKgLJASCxtjVHhtK03v1YR0Q3m2CN31hdAFW3FeQpw@mail.gmail.com>

volume_nuyl implements algorithm from http://dx.doi.org/10.1109/42.836373
volume_pol - is a simplified version of the same idea, fitting a straight
line (or n-degree polinomial) on quantiles of two scans.

On Mon, Jun 12, 2017 at 4:06 PM, Raquib Ridwan <raquib.ridwan at gmail.com>
wrote:

> Hi,
>
> I would like to know what volume_pol does for normalization. I seem to not
> find out any documentation of volume_pol and volume_nuyl
>
> *Sincerely,*
> *Abdur Raquib Ridwan, M.Sc *
> *PhD student at IIT(Chicago,USA)*
> *Research Assistant at MIRC*
> *Specialization in MRI imaging*
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com

From kw350 at cam.ac.uk  Wed Jun 21 14:24:31 2017
From: kw350 at cam.ac.uk (K. Wagstyl)
Date: Wed, 21 Jun 2017 14:24:31 -0400
Subject: [MINC-users] HDF5 target installation failure
Message-ID: <a83ce7b9b4ba772e36debbc9f2375fa1@cam.ac.uk>

Hello,

I have been trying to install the minc-toolkit-v2 from GitHub on my 
machine. However the installation fails on the HDF5 target:

[  2%] Performing download step (download, verify and extract) for 
'HDF5'
-- verifying file...
        
file='/homeb/jinm14/jinm1403/library_sources/minc-toolkit-v2/build/HDF5-prefix/src/hdf5-1.8.18.tar.bz2'
-- MD5 hash of
     
/homeb/jinm14/jinm1403/library_sources/minc-toolkit-v2/build/HDF5-prefix/src/hdf5-1.8.18.tar.bz2
   does not match expected value
     expected: '29117bf488887f89888f9304c8ebea0b'
       actual: 'd41d8cd98f00b204e9800998ecf8427e'
-- File already exists but hash mismatch. Removing...
-- downloading...
        
src='https://support.hdfgroup.org/ftp/HDF5/current18/src/hdf5-1.8.18.tar.bz2'
        
dst='/homeb/jinm14/jinm1403/library_sources/minc-toolkit-v2/build/HDF5-prefix/src/hdf5-1.8.18.tar.bz2'
        timeout='none'
error: downloading 
'https://support.hdfgroup.org/ftp/HDF5/current18/src/hdf5-1.8.18.tar.bz2' 
failed
   status_code: 22
   status_string: "HTTP response code said error"

I have checked the hdf5 version under this link was updated a few days 
ago to 1.8.19 . How do I tell make to use expect the new version? Should 
it be able to autodetect this?

Thanks,
Konrad (sent on behalf of Hannah Spitzer)


From bert at phalarope.com  Wed Jun 21 22:24:27 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Wed, 21 Jun 2017 22:24:27 -0400
Subject: [MINC-users] HDF5 target installation failure
In-Reply-To: <a83ce7b9b4ba772e36debbc9f2375fa1@cam.ac.uk>
References: <a83ce7b9b4ba772e36debbc9f2375fa1@cam.ac.uk>
Message-ID: <CAAd5DeSd90LNhYqd=HnVduLPNRQbF3EepYmvEp7hdAPLwEQVWw@mail.gmail.com>

Hi Konrad,

For some reason the HDF5 download is failing on that system - I think they
have released a new version recently, and rendered the old download link
obsolete.

Someone here will have to update the HDF5 link for minc-toolkit-v2

      -bert

On Wed, Jun 21, 2017 at 2:24 PM, K. Wagstyl <kw350 at cam.ac.uk> wrote:

> Hello,
>
> I have been trying to install the minc-toolkit-v2 from GitHub on my
> machine. However the installation fails on the HDF5 target:
>
> [  2%] Performing download step (download, verify and extract) for 'HDF5'
> -- verifying file...
>        file='/homeb/jinm14/jinm1403/library_sources/minc-toolkit-v
> 2/build/HDF5-prefix/src/hdf5-1.8.18.tar.bz2'
> -- MD5 hash of
>     /homeb/jinm14/jinm1403/library_sources/minc-toolkit-v2/
> build/HDF5-prefix/src/hdf5-1.8.18.tar.bz2
>   does not match expected value
>     expected: '29117bf488887f89888f9304c8ebea0b'
>       actual: 'd41d8cd98f00b204e9800998ecf8427e'
> -- File already exists but hash mismatch. Removing...
> -- downloading...
>        src='https://support.hdfgroup.org/ftp/HDF5/
> current18/src/hdf5-1.8.18.tar.bz2'
>        dst='/homeb/jinm14/jinm1403/library_sources/minc-toolkit-v2
> /build/HDF5-prefix/src/hdf5-1.8.18.tar.bz2'
>        timeout='none'
> error: downloading 'https://support.hdfgroup.org/
> ftp/HDF5/current18/src/hdf5-1.8.18.tar.bz2' failed
>   status_code: 22
>   status_string: "HTTP response code said error"
>
> I have checked the hdf5 version under this link was updated a few days ago
> to 1.8.19 . How do I tell make to use expect the new version? Should it be
> able to autodetect this?
>
> Thanks,
> Konrad (sent on behalf of Hannah Spitzer)
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From bert at phalarope.com  Fri Jun 23 09:22:45 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Fri, 23 Jun 2017 09:22:45 -0400
Subject: [MINC-users] HDF5 target installation failure
In-Reply-To: <CAAd5DeSd90LNhYqd=HnVduLPNRQbF3EepYmvEp7hdAPLwEQVWw@mail.gmail.com>
References: <a83ce7b9b4ba772e36debbc9f2375fa1@cam.ac.uk>
	<CAAd5DeSd90LNhYqd=HnVduLPNRQbF3EepYmvEp7hdAPLwEQVWw@mail.gmail.com>
Message-ID: <CAAd5DeS_FOUB3sbKF0eSdZvqWa-NfSDo-mtKpJT0NqYU+865iA@mail.gmail.com>

Hi again,

I've updated the link in the develop branch of minc-toolkit-v2 if you want
to give it another try.

    -bert

On Wed, Jun 21, 2017 at 10:24 PM, Robert D. Vincent <bert at phalarope.com>
wrote:

> Hi Konrad,
>
> For some reason the HDF5 download is failing on that system - I think they
> have released a new version recently, and rendered the old download link
> obsolete.
>
> Someone here will have to update the HDF5 link for minc-toolkit-v2
>
>       -bert
>
> On Wed, Jun 21, 2017 at 2:24 PM, K. Wagstyl <kw350 at cam.ac.uk> wrote:
>
>> Hello,
>>
>> I have been trying to install the minc-toolkit-v2 from GitHub on my
>> machine. However the installation fails on the HDF5 target:
>>
>> [  2%] Performing download step (download, verify and extract) for 'HDF5'
>> -- verifying file...
>>        file='/homeb/jinm14/jinm1403/library_sources/minc-toolkit-v
>> 2/build/HDF5-prefix/src/hdf5-1.8.18.tar.bz2'
>> -- MD5 hash of
>>     /homeb/jinm14/jinm1403/library_sources/minc-toolkit-v2/build
>> /HDF5-prefix/src/hdf5-1.8.18.tar.bz2
>>   does not match expected value
>>     expected: '29117bf488887f89888f9304c8ebea0b'
>>       actual: 'd41d8cd98f00b204e9800998ecf8427e'
>> -- File already exists but hash mismatch. Removing...
>> -- downloading...
>>        src='https://support.hdfgroup.org/ftp/HDF5/current18/src/
>> hdf5-1.8.18.tar.bz2'
>>        dst='/homeb/jinm14/jinm1403/library_sources/minc-toolkit-v2
>> /build/HDF5-prefix/src/hdf5-1.8.18.tar.bz2'
>>        timeout='none'
>> error: downloading 'https://support.hdfgroup.org/
>> ftp/HDF5/current18/src/hdf5-1.8.18.tar.bz2' failed
>>   status_code: 22
>>   status_string: "HTTP response code said error"
>>
>> I have checked the hdf5 version under this link was updated a few days
>> ago to 1.8.19 . How do I tell make to use expect the new version? Should it
>> be able to autodetect this?
>>
>> Thanks,
>> Konrad (sent on behalf of Hannah Spitzer)
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>

From h.spitzer at fz-juelich.de  Fri Jun 23 19:46:46 2017
From: h.spitzer at fz-juelich.de (Spitzer, Hannah)
Date: Fri, 23 Jun 2017 23:46:46 +0000
Subject: [MINC-users] HDF5 target installation failure
In-Reply-To: <CAAd5DeS_FOUB3sbKF0eSdZvqWa-NfSDo-mtKpJT0NqYU+865iA@mail.gmail.com>
References: <a83ce7b9b4ba772e36debbc9f2375fa1@cam.ac.uk>
	<CAAd5DeSd90LNhYqd=HnVduLPNRQbF3EepYmvEp7hdAPLwEQVWw@mail.gmail.com>,
	<CAAd5DeS_FOUB3sbKF0eSdZvqWa-NfSDo-mtKpJT0NqYU+865iA@mail.gmail.com>
Message-ID: <C25DD87F59451541A2F3E2C6D1328B3A2BB42F18@MBX2010-E01.ad.fz-juelich.de>

Hi Bert,

yes, the develop branch now works for me.

Thanks!
Hannah

________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of Robert D. Vincent [bert at phalarope.com]
Sent: Friday, June 23, 2017 3:22 PM
To: MINC users mailing list
Subject: Re: [MINC-users] HDF5 target installation failure

Hi again,

I've updated the link in the develop branch of minc-toolkit-v2 if you want
to give it another try.

    -bert

On Wed, Jun 21, 2017 at 10:24 PM, Robert D. Vincent <bert at phalarope.com>
wrote:

> Hi Konrad,
>
> For some reason the HDF5 download is failing on that system - I think they
> have released a new version recently, and rendered the old download link
> obsolete.
>
> Someone here will have to update the HDF5 link for minc-toolkit-v2
>
>       -bert
>
> On Wed, Jun 21, 2017 at 2:24 PM, K. Wagstyl <kw350 at cam.ac.uk> wrote:
>
>> Hello,
>>
>> I have been trying to install the minc-toolkit-v2 from GitHub on my
>> machine. However the installation fails on the HDF5 target:
>>
>> [  2%] Performing download step (download, verify and extract) for 'HDF5'
>> -- verifying file...
>>        file='/homeb/jinm14/jinm1403/library_sources/minc-toolkit-v
>> 2/build/HDF5-prefix/src/hdf5-1.8.18.tar.bz2'
>> -- MD5 hash of
>>     /homeb/jinm14/jinm1403/library_sources/minc-toolkit-v2/build
>> /HDF5-prefix/src/hdf5-1.8.18.tar.bz2
>>   does not match expected value
>>     expected: '29117bf488887f89888f9304c8ebea0b'
>>       actual: 'd41d8cd98f00b204e9800998ecf8427e'
>> -- File already exists but hash mismatch. Removing...
>> -- downloading...
>>        src='https://support.hdfgroup.org/ftp/HDF5/current18/src/
>> hdf5-1.8.18.tar.bz2'
>>        dst='/homeb/jinm14/jinm1403/library_sources/minc-toolkit-v2
>> /build/HDF5-prefix/src/hdf5-1.8.18.tar.bz2'
>>        timeout='none'
>> error: downloading 'https://support.hdfgroup.org/
>> ftp/HDF5/current18/src/hdf5-1.8.18.tar.bz2' failed
>>   status_code: 22
>>   status_string: "HTTP response code said error"
>>
>> I have checked the hdf5 version under this link was updated a few days
>> ago to 1.8.19 . How do I tell make to use expect the new version? Should it
>> be able to autodetect this?
>>
>> Thanks,
>> Konrad (sent on behalf of Hannah Spitzer)
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


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