From peter.wendorff at c-lab.de Tue Jun 4 08:26:49 2013 From: peter.wendorff at c-lab.de (Peter Wendorff) Date: Tue, 04 Jun 2013 14:26:49 +0200 Subject: [MINC-users] DEPRECATED warning in sharpen_volume Message-ID: <51ADDD09.5010209@c-lab.de> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi. I'm working with freesurfer as a software developer in a cloud project. My task is to enable control of freesurfer via network (e.g. REST interfaces). That works fine so far, but I stumbled over the following pearl deprecated warning, that originate from MRI, and for which the freesurfer mailing list people sent me to this list. The warning "Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer//mni/bin/sharpen_volume line 153." get's printed to the log files repeatingly. I'm not a pearl expert, but I think, it's due to a more up to date pearl version used here, that deprecated the usage of ? delimiters for patterns without explicit operator. Using / as a delimiter works fine. I changed that locally to (new line 153): ($output_volume =~ /^([\S]+).mnc/) && ($base_name = $1) || die "sharpen_volume failed: output volume does not appear to be" ." a minc volume.\n"; (the original code here was): ($output_volume =~ ?^([\S]+).mnc?) && ($base_name = $1) || die "sharpen_volume failed: output volume does not appear to be" ." a minc volume.\n"; I'm not sure this is the best solution. It's even not strictly necessary to change this - it's only a warning that's thrown; but I think, it's useful. How can I submit this as a patch? Is it enough to report it here? What to do? regards Peter Wendorff P.S.: For referene the header parameters of my sharpen_volume for revision comparison: #---------------------------------------------------------------------------- #$RCSfile: sharpen_volume.in,v $ #$Revision: 1.1 $ #$Author: bert $ #$Date: 2003/04/16 14:29:34 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header - ---------------------------------- #@NAME : sharpen_volume #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: modifies intensities so as to produce a sharper histogram #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : February 28, 1996 #@MODIFIED : #----------------------------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlGt3QMACgkQi8ffXNvWmYR6QQCfcWQpwuwK2TlpVLAmoLkH2h8M YaEAn2XAD8BEHn0qXwcgd/MQ7L+llCr9 =l2GU -----END PGP SIGNATURE----- From a.janke at gmail.com Tue Jun 4 08:36:41 2013 From: a.janke at gmail.com (Andrew Janke) Date: Tue, 4 Jun 2013 22:36:41 +1000 Subject: [MINC-users] DEPRECATED warning in sharpen_volume In-Reply-To: <51ADDD09.5010209@c-lab.de> References: <51ADDD09.5010209@c-lab.de> Message-ID: Hi Peter, > I'm working with freesurfer as a software developer in a cloud > project. My task is to enable control of freesurfer via network (e.g. > REST interfaces). > > That works fine so far, but I stumbled over the following pearl > deprecated warning, that originate from MRI, and for which the > freesurfer mailing list people sent me to this list. > The warning > > "Use of ?PATTERN? without explicit operator is deprecated at > /usr/local/freesurfer//mni/bin/sharpen_volume line 153." Thanks for the bug report. This has been corrected in the MINC github repository here: https://github.com/BIC-MNI/N3/commit/0fdb7b069afec6983d5aa0be1f9156266cef393b I don't have any control over which version(s) of the MINC tools freesurfer uses though! so can't update your version. Thanks a From matthijs at mouseimaging.ca Thu Jun 6 14:18:19 2013 From: matthijs at mouseimaging.ca (Matthijs Van Eede) Date: Thu, 6 Jun 2013 14:18:19 -0400 (EDT) Subject: [MINC-users] RMINC - Calculating p-value for the Wilcoxon test In-Reply-To: References: Message-ID: <48093602.144085.1370542699651.JavaMail.root@mouseimaging.ca> Greetings, I have a reply from Jason to this question, but I don't see it on the MINC-users list, so just in case here was his answer: *** Use the pwilcox function - pass it the vector of W values from minc.model and the size of each of your two groups. Jason *** Cheers, Matthijs ----- Original Message ----- From: "Tom Beaudry" To: "MINC users mailing list" Sent: Monday, May 27, 2013 2:34:51 PM Subject: [MINC-users] RMINC - Calculating p-value for the Wilcoxon test Hi, I am using RMINC to calculate the W value for an analysis with group sizes of 6 and 19. I then get some W values (from 1-114), but how can I calculate the associated p-value from the W-Value? This is the R code that I am using: rm(list=ls(all=TRUE)) library(RMINC) gf1 <- read.csv("input.csv") vs1 <- minc.model(gf1$FA, gf1$group, "wilcoxon") vs1[is.na(vs1)] <- 0 mincWriteVolume(vs1, "output.mnc", gf1$FA) thanks for the help! Thomas Beaudry _______________________________________________ MINC-users at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From waveflux at gmail.com Thu Jun 6 14:26:09 2013 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 6 Jun 2013 14:26:09 -0400 Subject: [MINC-users] RMINC - Calculating p-value for the Wilcoxon test In-Reply-To: <48093602.144085.1370542699651.JavaMail.root@mouseimaging.ca> References: <48093602.144085.1370542699651.JavaMail.root@mouseimaging.ca> Message-ID: thanks for the answer! On Thu, Jun 6, 2013 at 2:18 PM, Matthijs Van Eede wrote: > Greetings, > > I have a reply from Jason to this question, but I don't see it on the > MINC-users list, so just in case here was his answer: > > *** > Use the pwilcox function - pass it the vector of W values from minc.model > and the size of each of your two groups. > > Jason > *** > > Cheers, > Matthijs > > ----- Original Message ----- > From: "Tom Beaudry" > To: "MINC users mailing list" > Sent: Monday, May 27, 2013 2:34:51 PM > Subject: [MINC-users] RMINC - Calculating p-value for the Wilcoxon test > > Hi, > > I am using RMINC to calculate the W value for an analysis with group sizes > of 6 and 19. I then get some W values (from 1-114), but how can I calculate > the associated p-value from the W-Value? > > This is the R code that I am using: > > rm(list=ls(all=TRUE)) > library(RMINC) > gf1 <- read.csv("input.csv") > vs1 <- minc.model(gf1$FA, gf1$group, "wilcoxon") > vs1[is.na(vs1)] <- 0 > mincWriteVolume(vs1, "output.mnc", gf1$FA) > > thanks for the help! > Thomas Beaudry > _______________________________________________ > 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 pierre.bellec at gmail.com Sun Jun 9 23:49:49 2013 From: pierre.bellec at gmail.com (Pierre Bellec) Date: Sun, 9 Jun 2013 23:49:49 -0400 Subject: [MINC-users] Grunge Gala, Brain-Art Competition Gallery, and art exhibition at OHBM Message-ID: * Dear Minc users, In the tradition of past Neuro Bureau gala events in Barcelona, Quebec City, and Beijing, we are excited to announce the upcoming Grunge Gala (Smells like brain spirit!) next week at the OHBM conference in Seattle. The party will be held on Monday, June 17th, at The Crocodile. The winners of the 2013 Brain-Art Competition will be announced (2013 submissions gallery has been launched!). And in the spirit of Seattle and data sharing, we?ll be holding an open-mic at the event where all are welcome to come and perform. Throughout the week, we also invite you to visit the art exhibition entitled ?Subjective Resonance Imaging?, curated by Noah Hutton at the conference center. We are grateful to our official sponsors: The International NeuroImaging Data-Sharing Initiative (INDI), The Child Mind Institute, Frontiers, and the Max Planck Institute for Human Cognitive and Brain Sciences for helping to make these initiatives possible. If you would like to help support the dialogue between art and neuroscience, and might be interested in picking up a copy of the exhibition catalogue along the way, you still have one day left: http://indiegogo.com/projects/neurobureau-art-at-hbm-2013/ More information about the party at OHBM, the 2013 Brain-Art Competition Gallery, and the art exhibition, is available at: www.neurobureau.org* * * Pierre Bellec and the Neurobureau From sebastien.proulx2 at mcgill.ca Thu Jun 20 14:00:43 2013 From: sebastien.proulx2 at mcgill.ca (=?windows-1252?Q?S=E9bastien_Proulx?=) Date: Thu, 20 Jun 2013 14:00:43 -0400 Subject: [MINC-users] mincresample apply nonlinear transformation using .xfm with Transform Type = Grid_Transform In-Reply-To: References: Message-ID: <51C3434B.2030406@mcgill.ca> Hello Minc people, My colleague gave me transformation files from a nonlinear registration to a template done with minctools. I'm trying to use those to bring some images (segmented in MNI space) back to their native space. Linear transforms are working fine, but I apply the inverse of the nonlinear part: mincresample -inverse_transformation -transformation nonLinTransformFileName.xfm -like nativeSpaceAnatomic.mnc templateSpaceSegmentedImage.mnc nativeSpaceSegmentedImage.mnc doesn't work whatever I do (reloading files or try simple variants of the command): Error: opening MINC file "./TMS_CON_44_nlfit_It_grid_0.mnc". input_transform: error reading transform. Error reading transformation file. Here is the content of nonLinTransformFileName.xfm: --------------------------------------------------------------------------------------------------- MNI Transform File %Sun Aug 5 12:30:27 2012>>> minctracc -clobber -nonlinear corrcoeff -weight 1 -stiffness 1 -similarity 0.3 -sub_lattice 6 -iterations 10 -step 4 4 4 -lattice_diam 12 12 12 -transformation /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_4.xfm -source_mask /sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/mask/TMS_CON_44_skull_mask.mnc -model_mask /sb/home/prioux/tools/CIVET/Feb-2010-a/share/mni-models//icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_2_blur.mnc /tmp/best1stepnlreg.pl-UAIGq86o/Ticbm_avg_152_t1_tal_nlin_symmetric_VI_2_blur.mnc/sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/transforms/nonlinear/TMS_CON_44_nlfit_It.xfm %(Package mni_autoreg 0.99.3, compiled by tnguyen at localhost.localdomain (x86_64-unknown-linux-gnu) on Mon Aug 30 17:14:08 EDT 2010) Transform_Type = Linear; Linear_Transform = 1 0 0 0 0 1 0 0 0 0 1 0; Transform_Type = Grid_Transform; Displacement_Volume = TMS_CON_44_nlfit_It_grid_0.mnc; --------------------------------------------------------------------------------------------------- Is there something I'm missing, like non linear transformations use another command? Note that I cannot open TMS_CON_44_nlfit_It_grid_0.mnc with register either, but I bet this is expected... Thanks a lot for your help, I really have no idea what to do with that... apart from rerunning the segmentation in native space! S?bastien Proulx, MSc Research Assistant McGill University (514) 398-6644 #00445 From zijdenbos at gmail.com Thu Jun 20 14:22:39 2013 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Thu, 20 Jun 2013 14:22:39 -0400 Subject: [MINC-users] mincresample apply nonlinear transformation using .xfm with Transform Type = Grid_Transform In-Reply-To: <51C3434B.2030406@mcgill.ca> References: <51C3434B.2030406@mcgill.ca> Message-ID: Hi S?bastien, My guess would be that the deformation field (grid_0.mnc) file is corrupt. What happens when you run this: minccomplete TMS_CON_44_nlfit_It_grid_0.mnc and/or mincfinfo? -- A On Thu, Jun 20, 2013 at 2:00 PM, S?bastien Proulx wrote: > Hello Minc people, > > My colleague gave me transformation files from a nonlinear registration to a > template done with minctools. I'm trying to use those to bring some images > (segmented in MNI space) back to their native space. Linear transforms are > working fine, but I apply the inverse of the nonlinear part: > > mincresample -inverse_transformation -transformation > nonLinTransformFileName.xfm -like nativeSpaceAnatomic.mnc > templateSpaceSegmentedImage.mnc nativeSpaceSegmentedImage.mnc > > > doesn't work whatever I do (reloading files or try simple variants of the > command): > > Error: opening MINC file "./TMS_CON_44_nlfit_It_grid_0.mnc". > input_transform: error reading transform. > Error reading transformation file. > > > Here is the content of nonLinTransformFileName.xfm: > --------------------------------------------------------------------------------------------------- > MNI Transform File > %Sun Aug 5 12:30:27 2012>>> minctracc -clobber -nonlinear corrcoeff -weight > 1 -stiffness 1 -similarity 0.3 -sub_lattice 6 -iterations 10 -step 4 4 4 > -lattice_diam 12 12 12 -transformation > /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_4.xfm -source_mask > /sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/mask/TMS_CON_44_skull_mask.mnc > -model_mask > /sb/home/prioux/tools/CIVET/Feb-2010-a/share/mni-models//icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc > /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_2_blur.mnc > /tmp/best1stepnlreg.pl-UAIGq86o/Ticbm_avg_152_t1_tal_nlin_symmetric_VI_2_blur.mnc/sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/transforms/nonlinear/TMS_CON_44_nlfit_It.xfm > %(Package mni_autoreg 0.99.3, compiled by tnguyen at localhost.localdomain > (x86_64-unknown-linux-gnu) on Mon Aug 30 17:14:08 EDT 2010) > > Transform_Type = Linear; > Linear_Transform = > 1 0 0 0 > 0 1 0 0 > 0 0 1 0; > Transform_Type = Grid_Transform; > Displacement_Volume = TMS_CON_44_nlfit_It_grid_0.mnc; > --------------------------------------------------------------------------------------------------- > > > Is there something I'm missing, like non linear transformations use another > command? Note that I cannot open TMS_CON_44_nlfit_It_grid_0.mnc with > register either, but I bet this is expected... > > Thanks a lot for your help, I really have no idea what to do with that... > apart from rerunning the segmentation in native space! > > S?bastien Proulx, MSc > Research Assistant > McGill University > (514) 398-6644 #00445 > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sebastien.proulx2 at mcgill.ca Thu Jun 20 15:31:33 2013 From: sebastien.proulx2 at mcgill.ca (=?ISO-8859-1?Q?S=E9bastien_Proulx?=) Date: Thu, 20 Jun 2013 15:31:33 -0400 Subject: [MINC-users] mincresample apply nonlinear transformation using .xfm with Transform Type = Grid_Transform In-Reply-To: References: <51C3434B.2030406@mcgill.ca> Message-ID: <51C35895.90703@mcgill.ca> It seems like I don't have access to minccomplete, but see the following terminal output: ------------------------------------------------------------------------------------- duncan:~/transformTest_bis/Transforms_45/nonlinear> mincomplete TMS_CON_45_nlfit_It_grid_0.mnc mincomplete: Command not found. duncan:~/transformTest_bis/Transforms_45/nonlinear> mincinfo TMS_CON_45_nlfit_It_grid_0.mnc ncopen: filename "TMS_CON_45_nlfit_It_grid_0.mnc": NetCDF: Unknown file format miopen: MINC package entry point ------------------------------------------------------------------------------------- Since I tried with two different subjects, I thought a corruption was unlikely, but I guess mincinfo should be able to read any intact minc file. Is it possible that minctracc (see content of .xfm) did correctly produce the nonlinearly registered images, but somehow screwed-up all the ..._nlfit_It_grid_0.mnc files? Thanks a lot Alex! S?bastien Proulx, MSc Research Assistant McGill University (514) 398-6644 #00445 Le 13-06-20 2:22 PM, Alex Zijdenbos a ?crit : > Hi S?bastien, > > My guess would be that the deformation field (grid_0.mnc) file is > corrupt. What happens when you run this: > > minccomplete TMS_CON_44_nlfit_It_grid_0.mnc > > and/or mincfinfo? > > -- A > > On Thu, Jun 20, 2013 at 2:00 PM, S?bastien Proulx > wrote: >> Hello Minc people, >> >> My colleague gave me transformation files from a nonlinear registration to a >> template done with minctools. I'm trying to use those to bring some images >> (segmented in MNI space) back to their native space. Linear transforms are >> working fine, but I apply the inverse of the nonlinear part: >> >> mincresample -inverse_transformation -transformation >> nonLinTransformFileName.xfm -like nativeSpaceAnatomic.mnc >> templateSpaceSegmentedImage.mnc nativeSpaceSegmentedImage.mnc >> >> >> doesn't work whatever I do (reloading files or try simple variants of the >> command): >> >> Error: opening MINC file "./TMS_CON_44_nlfit_It_grid_0.mnc". >> input_transform: error reading transform. >> Error reading transformation file. >> >> >> Here is the content of nonLinTransformFileName.xfm: >> --------------------------------------------------------------------------------------------------- >> MNI Transform File >> %Sun Aug 5 12:30:27 2012>>> minctracc -clobber -nonlinear corrcoeff -weight >> 1 -stiffness 1 -similarity 0.3 -sub_lattice 6 -iterations 10 -step 4 4 4 >> -lattice_diam 12 12 12 -transformation >> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_4.xfm -source_mask >> /sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/mask/TMS_CON_44_skull_mask.mnc >> -model_mask >> /sb/home/prioux/tools/CIVET/Feb-2010-a/share/mni-models//icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc >> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_2_blur.mnc >> /tmp/best1stepnlreg.pl-UAIGq86o/Ticbm_avg_152_t1_tal_nlin_symmetric_VI_2_blur.mnc/sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/transforms/nonlinear/TMS_CON_44_nlfit_It.xfm >> %(Package mni_autoreg 0.99.3, compiled by tnguyen at localhost.localdomain >> (x86_64-unknown-linux-gnu) on Mon Aug 30 17:14:08 EDT 2010) >> >> Transform_Type = Linear; >> Linear_Transform = >> 1 0 0 0 >> 0 1 0 0 >> 0 0 1 0; >> Transform_Type = Grid_Transform; >> Displacement_Volume = TMS_CON_44_nlfit_It_grid_0.mnc; >> --------------------------------------------------------------------------------------------------- >> >> >> Is there something I'm missing, like non linear transformations use another >> command? Note that I cannot open TMS_CON_44_nlfit_It_grid_0.mnc with >> register either, but I bet this is expected... >> >> Thanks a lot for your help, I really have no idea what to do with that... >> apart from rerunning the segmentation in native space! >> >> S?bastien Proulx, MSc >> Research Assistant >> McGill University >> (514) 398-6644 #00445 >> >> _______________________________________________ >> 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 zijdenbos at gmail.com Thu Jun 20 15:44:55 2013 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Thu, 20 Jun 2013 15:44:55 -0400 Subject: [MINC-users] mincresample apply nonlinear transformation using .xfm with Transform Type = Grid_Transform In-Reply-To: <51C35895.90703@mcgill.ca> References: <51C3434B.2030406@mcgill.ca> <51C35895.90703@mcgill.ca> Message-ID: 'minccomplete' has two 'c's :) you get the same error for all grid_0.mnc files, or just one? my other guess would be you are looking at a MINC1/MINC2 issue, and/or that you might have an ancient MINC install. What does 'mincresample -version' tell you? On Thu, Jun 20, 2013 at 3:31 PM, S?bastien Proulx wrote: > It seems like I don't have access to minccomplete, but see the following > terminal output: > ------------------------------------------------------------------------------------- > duncan:~/transformTest_bis/Transforms_45/nonlinear> mincomplete > TMS_CON_45_nlfit_It_grid_0.mnc > mincomplete: Command not found. > duncan:~/transformTest_bis/Transforms_45/nonlinear> mincinfo > TMS_CON_45_nlfit_It_grid_0.mnc > ncopen: filename "TMS_CON_45_nlfit_It_grid_0.mnc": NetCDF: Unknown file > format > miopen: MINC package entry point > ------------------------------------------------------------------------------------- > > Since I tried with two different subjects, I thought a corruption was > unlikely, but I guess mincinfo should be able to read any intact minc file. > Is it possible that minctracc (see content of .xfm) did correctly produce > the nonlinearly registered images, but somehow screwed-up all the > ..._nlfit_It_grid_0.mnc files? > > Thanks a lot Alex! > > > S?bastien Proulx, MSc > Research Assistant > McGill University > (514) 398-6644 #00445 > > Le 13-06-20 2:22 PM, Alex Zijdenbos a ?crit : >> >> Hi S?bastien, >> >> My guess would be that the deformation field (grid_0.mnc) file is >> corrupt. What happens when you run this: >> >> minccomplete TMS_CON_44_nlfit_It_grid_0.mnc >> >> and/or mincfinfo? >> >> -- A >> >> On Thu, Jun 20, 2013 at 2:00 PM, S?bastien Proulx >> wrote: >>> >>> Hello Minc people, >>> >>> My colleague gave me transformation files from a nonlinear registration >>> to a >>> template done with minctools. I'm trying to use those to bring some >>> images >>> (segmented in MNI space) back to their native space. Linear transforms >>> are >>> working fine, but I apply the inverse of the nonlinear part: >>> >>> mincresample -inverse_transformation -transformation >>> nonLinTransformFileName.xfm -like nativeSpaceAnatomic.mnc >>> templateSpaceSegmentedImage.mnc nativeSpaceSegmentedImage.mnc >>> >>> >>> doesn't work whatever I do (reloading files or try simple variants of the >>> command): >>> >>> Error: opening MINC file "./TMS_CON_44_nlfit_It_grid_0.mnc". >>> input_transform: error reading transform. >>> Error reading transformation file. >>> >>> >>> Here is the content of nonLinTransformFileName.xfm: >>> >>> --------------------------------------------------------------------------------------------------- >>> MNI Transform File >>> %Sun Aug 5 12:30:27 2012>>> minctracc -clobber -nonlinear corrcoeff >>> -weight >>> 1 -stiffness 1 -similarity 0.3 -sub_lattice 6 -iterations 10 -step 4 4 4 >>> -lattice_diam 12 12 12 -transformation >>> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_4.xfm -source_mask >>> >>> /sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/mask/TMS_CON_44_skull_mask.mnc >>> -model_mask >>> >>> /sb/home/prioux/tools/CIVET/Feb-2010-a/share/mni-models//icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc >>> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_2_blur.mnc >>> >>> /tmp/best1stepnlreg.pl-UAIGq86o/Ticbm_avg_152_t1_tal_nlin_symmetric_VI_2_blur.mnc/sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/transforms/nonlinear/TMS_CON_44_nlfit_It.xfm >>> %(Package mni_autoreg 0.99.3, compiled by tnguyen at localhost.localdomain >>> (x86_64-unknown-linux-gnu) on Mon Aug 30 17:14:08 EDT 2010) >>> >>> Transform_Type = Linear; >>> Linear_Transform = >>> 1 0 0 0 >>> 0 1 0 0 >>> 0 0 1 0; >>> Transform_Type = Grid_Transform; >>> Displacement_Volume = TMS_CON_44_nlfit_It_grid_0.mnc; >>> >>> --------------------------------------------------------------------------------------------------- >>> >>> >>> Is there something I'm missing, like non linear transformations use >>> another >>> command? Note that I cannot open TMS_CON_44_nlfit_It_grid_0.mnc with >>> register either, but I bet this is expected... >>> >>> Thanks a lot for your help, I really have no idea what to do with that... >>> apart from rerunning the segmentation in native space! >>> >>> S?bastien Proulx, MSc >>> Research Assistant >>> McGill University >>> (514) 398-6644 #00445 >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From sebastien.proulx2 at mcgill.ca Thu Jun 20 16:03:04 2013 From: sebastien.proulx2 at mcgill.ca (=?ISO-8859-1?Q?S=E9bastien_Proulx?=) Date: Thu, 20 Jun 2013 16:03:04 -0400 Subject: [MINC-users] mincresample apply nonlinear transformation using .xfm with Transform Type = Grid_Transform In-Reply-To: References: <51C3434B.2030406@mcgill.ca> <51C35895.90703@mcgill.ca> Message-ID: <51C35FF8.6060003@mcgill.ca> It's not me who did the registration, I'm only trying to undo it :-P (apply the inverse transform). My colleague gave me one subject, didn't work. He sent it again along with another subject, didn't work either for both. He could send me more, but I guess it would be the same. Same thing with min_cc_omplete. Trying stuff around, I copypasted the wrong lines. As for the version: duncan:~/transformTest_bis/Transforms_45/nonlinear> mincresample -version program: 1.5.1 libminc: 1.5.1 netcdf : "3.6.3" of May 20 2011 16:00:48 $ S?bastien Proulx, MSc Research Assistant McGill University (514) 398-6644 #00445 Le 13-06-20 3:44 PM, Alex Zijdenbos a ?crit : > 'minccomplete' has two 'c's :) > > you get the same error for all grid_0.mnc files, or just one? > > my other guess would be you are looking at a MINC1/MINC2 issue, and/or > that you might have an ancient MINC install. What does 'mincresample > -version' tell you? > > On Thu, Jun 20, 2013 at 3:31 PM, S?bastien Proulx > wrote: >> It seems like I don't have access to minccomplete, but see the following >> terminal output: >> ------------------------------------------------------------------------------------- >> duncan:~/transformTest_bis/Transforms_45/nonlinear> mincomplete >> TMS_CON_45_nlfit_It_grid_0.mnc >> mincomplete: Command not found. >> duncan:~/transformTest_bis/Transforms_45/nonlinear> mincinfo >> TMS_CON_45_nlfit_It_grid_0.mnc >> ncopen: filename "TMS_CON_45_nlfit_It_grid_0.mnc": NetCDF: Unknown file >> format >> miopen: MINC package entry point >> ------------------------------------------------------------------------------------- >> >> Since I tried with two different subjects, I thought a corruption was >> unlikely, but I guess mincinfo should be able to read any intact minc file. >> Is it possible that minctracc (see content of .xfm) did correctly produce >> the nonlinearly registered images, but somehow screwed-up all the >> ..._nlfit_It_grid_0.mnc files? >> >> Thanks a lot Alex! >> >> >> S?bastien Proulx, MSc >> Research Assistant >> McGill University >> (514) 398-6644 #00445 >> >> Le 13-06-20 2:22 PM, Alex Zijdenbos a ?crit : >>> Hi S?bastien, >>> >>> My guess would be that the deformation field (grid_0.mnc) file is >>> corrupt. What happens when you run this: >>> >>> minccomplete TMS_CON_44_nlfit_It_grid_0.mnc >>> >>> and/or mincfinfo? >>> >>> -- A >>> >>> On Thu, Jun 20, 2013 at 2:00 PM, S?bastien Proulx >>> wrote: >>>> Hello Minc people, >>>> >>>> My colleague gave me transformation files from a nonlinear registration >>>> to a >>>> template done with minctools. I'm trying to use those to bring some >>>> images >>>> (segmented in MNI space) back to their native space. Linear transforms >>>> are >>>> working fine, but I apply the inverse of the nonlinear part: >>>> >>>> mincresample -inverse_transformation -transformation >>>> nonLinTransformFileName.xfm -like nativeSpaceAnatomic.mnc >>>> templateSpaceSegmentedImage.mnc nativeSpaceSegmentedImage.mnc >>>> >>>> >>>> doesn't work whatever I do (reloading files or try simple variants of the >>>> command): >>>> >>>> Error: opening MINC file "./TMS_CON_44_nlfit_It_grid_0.mnc". >>>> input_transform: error reading transform. >>>> Error reading transformation file. >>>> >>>> >>>> Here is the content of nonLinTransformFileName.xfm: >>>> >>>> --------------------------------------------------------------------------------------------------- >>>> MNI Transform File >>>> %Sun Aug 5 12:30:27 2012>>> minctracc -clobber -nonlinear corrcoeff >>>> -weight >>>> 1 -stiffness 1 -similarity 0.3 -sub_lattice 6 -iterations 10 -step 4 4 4 >>>> -lattice_diam 12 12 12 -transformation >>>> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_4.xfm -source_mask >>>> >>>> /sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/mask/TMS_CON_44_skull_mask.mnc >>>> -model_mask >>>> >>>> /sb/home/prioux/tools/CIVET/Feb-2010-a/share/mni-models//icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc >>>> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_2_blur.mnc >>>> >>>> /tmp/best1stepnlreg.pl-UAIGq86o/Ticbm_avg_152_t1_tal_nlin_symmetric_VI_2_blur.mnc/sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/transforms/nonlinear/TMS_CON_44_nlfit_It.xfm >>>> %(Package mni_autoreg 0.99.3, compiled by tnguyen at localhost.localdomain >>>> (x86_64-unknown-linux-gnu) on Mon Aug 30 17:14:08 EDT 2010) >>>> >>>> Transform_Type = Linear; >>>> Linear_Transform = >>>> 1 0 0 0 >>>> 0 1 0 0 >>>> 0 0 1 0; >>>> Transform_Type = Grid_Transform; >>>> Displacement_Volume = TMS_CON_44_nlfit_It_grid_0.mnc; >>>> >>>> --------------------------------------------------------------------------------------------------- >>>> >>>> >>>> Is there something I'm missing, like non linear transformations use >>>> another >>>> command? Note that I cannot open TMS_CON_44_nlfit_It_grid_0.mnc with >>>> register either, but I bet this is expected... >>>> >>>> Thanks a lot for your help, I really have no idea what to do with that... >>>> apart from rerunning the segmentation in native space! >>>> >>>> S?bastien Proulx, MSc >>>> Research Assistant >>>> McGill University >>>> (514) 398-6644 #00445 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> _______________________________________________ >> 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 vladimir.fonov at gmail.com Thu Jun 20 16:35:55 2013 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 20 Jun 2013 16:35:55 -0400 Subject: [MINC-users] mincresample apply nonlinear transformation using .xfm with Transform Type = Grid_Transform In-Reply-To: <51C35FF8.6060003@mcgill.ca> References: <51C3434B.2030406@mcgill.ca> <51C35895.90703@mcgill.ca> <51C35FF8.6060003@mcgill.ca> Message-ID: <51C367AB.3080305@gmail.com> Hello, It looks like you received grid files in minc2 file format. And your computer (duncan) have minc1 installed. On 13-06-20 04:03 PM, S?bastien Proulx wrote: > It's not me who did the registration, I'm only trying to undo it :-P > (apply the inverse transform). My colleague gave me one subject, didn't > work. He sent it again along with another subject, didn't work either > for both. He could send me more, but I guess it would be the same. > > Same thing with min_cc_omplete. Trying stuff around, I copypasted the > wrong lines. > > As for the version: > duncan:~/transformTest_bis/Transforms_45/nonlinear> mincresample -version > program: 1.5.1 > libminc: 1.5.1 > netcdf : "3.6.3" of May 20 2011 16:00:48 $ > > S?bastien Proulx, MSc > Research Assistant > McGill University > (514) 398-6644 #00445 > > Le 13-06-20 3:44 PM, Alex Zijdenbos a ?crit : >> 'minccomplete' has two 'c's :) >> >> you get the same error for all grid_0.mnc files, or just one? >> >> my other guess would be you are looking at a MINC1/MINC2 issue, and/or >> that you might have an ancient MINC install. What does 'mincresample >> -version' tell you? >> >> On Thu, Jun 20, 2013 at 3:31 PM, S?bastien Proulx >> wrote: >>> It seems like I don't have access to minccomplete, but see the following >>> terminal output: >>> ------------------------------------------------------------------------------------- >>> >>> duncan:~/transformTest_bis/Transforms_45/nonlinear> mincomplete >>> TMS_CON_45_nlfit_It_grid_0.mnc >>> mincomplete: Command not found. >>> duncan:~/transformTest_bis/Transforms_45/nonlinear> mincinfo >>> TMS_CON_45_nlfit_It_grid_0.mnc >>> ncopen: filename "TMS_CON_45_nlfit_It_grid_0.mnc": NetCDF: Unknown file >>> format >>> miopen: MINC package entry point >>> ------------------------------------------------------------------------------------- >>> >>> >>> Since I tried with two different subjects, I thought a corruption was >>> unlikely, but I guess mincinfo should be able to read any intact minc >>> file. >>> Is it possible that minctracc (see content of .xfm) did correctly >>> produce >>> the nonlinearly registered images, but somehow screwed-up all the >>> ..._nlfit_It_grid_0.mnc files? >>> >>> Thanks a lot Alex! >>> >>> >>> S?bastien Proulx, MSc >>> Research Assistant >>> McGill University >>> (514) 398-6644 #00445 >>> >>> Le 13-06-20 2:22 PM, Alex Zijdenbos a ?crit : >>>> Hi S?bastien, >>>> >>>> My guess would be that the deformation field (grid_0.mnc) file is >>>> corrupt. What happens when you run this: >>>> >>>> minccomplete TMS_CON_44_nlfit_It_grid_0.mnc >>>> >>>> and/or mincfinfo? >>>> >>>> -- A >>>> >>>> On Thu, Jun 20, 2013 at 2:00 PM, S?bastien Proulx >>>> wrote: >>>>> Hello Minc people, >>>>> >>>>> My colleague gave me transformation files from a nonlinear >>>>> registration >>>>> to a >>>>> template done with minctools. I'm trying to use those to bring some >>>>> images >>>>> (segmented in MNI space) back to their native space. Linear transforms >>>>> are >>>>> working fine, but I apply the inverse of the nonlinear part: >>>>> >>>>> mincresample -inverse_transformation -transformation >>>>> nonLinTransformFileName.xfm -like nativeSpaceAnatomic.mnc >>>>> templateSpaceSegmentedImage.mnc nativeSpaceSegmentedImage.mnc >>>>> >>>>> >>>>> doesn't work whatever I do (reloading files or try simple variants >>>>> of the >>>>> command): >>>>> >>>>> Error: opening MINC file "./TMS_CON_44_nlfit_It_grid_0.mnc". >>>>> input_transform: error reading transform. >>>>> Error reading transformation file. >>>>> >>>>> >>>>> Here is the content of nonLinTransformFileName.xfm: >>>>> >>>>> --------------------------------------------------------------------------------------------------- >>>>> >>>>> MNI Transform File >>>>> %Sun Aug 5 12:30:27 2012>>> minctracc -clobber -nonlinear corrcoeff >>>>> -weight >>>>> 1 -stiffness 1 -similarity 0.3 -sub_lattice 6 -iterations 10 -step >>>>> 4 4 4 >>>>> -lattice_diam 12 12 12 -transformation >>>>> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_4.xfm >>>>> -source_mask >>>>> >>>>> /sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/mask/TMS_CON_44_skull_mask.mnc >>>>> >>>>> -model_mask >>>>> >>>>> /sb/home/prioux/tools/CIVET/Feb-2010-a/share/mni-models//icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc >>>>> >>>>> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_2_blur.mnc >>>>> >>>>> /tmp/best1stepnlreg.pl-UAIGq86o/Ticbm_avg_152_t1_tal_nlin_symmetric_VI_2_blur.mnc/sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/transforms/nonlinear/TMS_CON_44_nlfit_It.xfm >>>>> >>>>> %(Package mni_autoreg 0.99.3, compiled by >>>>> tnguyen at localhost.localdomain >>>>> (x86_64-unknown-linux-gnu) on Mon Aug 30 17:14:08 EDT 2010) >>>>> >>>>> Transform_Type = Linear; >>>>> Linear_Transform = >>>>> 1 0 0 0 >>>>> 0 1 0 0 >>>>> 0 0 1 0; >>>>> Transform_Type = Grid_Transform; >>>>> Displacement_Volume = TMS_CON_44_nlfit_It_grid_0.mnc; -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From mferre at bic.mni.mcgill.ca Thu Jun 20 16:40:26 2013 From: mferre at bic.mni.mcgill.ca (Michael Ferreira) Date: Thu, 20 Jun 2013 16:40:26 -0400 Subject: [MINC-users] mincresample apply nonlinear transformation using .xfm with Transform Type = Grid_Transform In-Reply-To: <51C367AB.3080305@gmail.com> References: <51C3434B.2030406@mcgill.ca> <51C35895.90703@mcgill.ca> <51C35FF8.6060003@mcgill.ca> <51C367AB.3080305@gmail.com> Message-ID: <51C368BA.9080404@bic.mni.mcgill.ca> Hi Sebas, Since I see from your BIC home directory that you are a bash shell user, type this: export PATH='/usr/local/bic/bin:'$PATH Then retry your mincresample command, it should work now. Your output will be in MINC2 format though, so it may be wise to always use MINC2. To do this, add the above PATH definition to your ~/.bashrc file. This way, every time you login to the BIC you will be using the MINC2 tools. Regards, mike On 20/06/13 04:35 PM, Vladimir S. FONOV wrote: > Hello, > > > It looks like you received grid files in minc2 file format. And your > computer (duncan) have minc1 installed. > > On 13-06-20 04:03 PM, S?bastien Proulx wrote: >> It's not me who did the registration, I'm only trying to undo it :-P >> (apply the inverse transform). My colleague gave me one subject, didn't >> work. He sent it again along with another subject, didn't work either >> for both. He could send me more, but I guess it would be the same. >> >> Same thing with min_cc_omplete. Trying stuff around, I copypasted the >> wrong lines. >> >> As for the version: >> duncan:~/transformTest_bis/Transforms_45/nonlinear> mincresample -version >> program: 1.5.1 >> libminc: 1.5.1 >> netcdf : "3.6.3" of May 20 2011 16:00:48 $ >> >> S?bastien Proulx, MSc >> Research Assistant >> McGill University >> (514) 398-6644 #00445 >> >> Le 13-06-20 3:44 PM, Alex Zijdenbos a ?crit : >>> 'minccomplete' has two 'c's :) >>> >>> you get the same error for all grid_0.mnc files, or just one? >>> >>> my other guess would be you are looking at a MINC1/MINC2 issue, and/or >>> that you might have an ancient MINC install. What does 'mincresample >>> -version' tell you? >>> >>> On Thu, Jun 20, 2013 at 3:31 PM, S?bastien Proulx >>> wrote: >>>> It seems like I don't have access to minccomplete, but see the >>>> following >>>> terminal output: >>>> ------------------------------------------------------------------------------------- >>>> >>>> >>>> duncan:~/transformTest_bis/Transforms_45/nonlinear> mincomplete >>>> TMS_CON_45_nlfit_It_grid_0.mnc >>>> mincomplete: Command not found. >>>> duncan:~/transformTest_bis/Transforms_45/nonlinear> mincinfo >>>> TMS_CON_45_nlfit_It_grid_0.mnc >>>> ncopen: filename "TMS_CON_45_nlfit_It_grid_0.mnc": NetCDF: Unknown file >>>> format >>>> miopen: MINC package entry point >>>> ------------------------------------------------------------------------------------- >>>> >>>> >>>> >>>> Since I tried with two different subjects, I thought a corruption was >>>> unlikely, but I guess mincinfo should be able to read any intact minc >>>> file. >>>> Is it possible that minctracc (see content of .xfm) did correctly >>>> produce >>>> the nonlinearly registered images, but somehow screwed-up all the >>>> ..._nlfit_It_grid_0.mnc files? >>>> >>>> Thanks a lot Alex! >>>> >>>> >>>> S?bastien Proulx, MSc >>>> Research Assistant >>>> McGill University >>>> (514) 398-6644 #00445 >>>> >>>> Le 13-06-20 2:22 PM, Alex Zijdenbos a ?crit : >>>>> Hi S?bastien, >>>>> >>>>> My guess would be that the deformation field (grid_0.mnc) file is >>>>> corrupt. What happens when you run this: >>>>> >>>>> minccomplete TMS_CON_44_nlfit_It_grid_0.mnc >>>>> >>>>> and/or mincfinfo? >>>>> >>>>> -- A >>>>> >>>>> On Thu, Jun 20, 2013 at 2:00 PM, S?bastien Proulx >>>>> wrote: >>>>>> Hello Minc people, >>>>>> >>>>>> My colleague gave me transformation files from a nonlinear >>>>>> registration >>>>>> to a >>>>>> template done with minctools. I'm trying to use those to bring some >>>>>> images >>>>>> (segmented in MNI space) back to their native space. Linear >>>>>> transforms >>>>>> are >>>>>> working fine, but I apply the inverse of the nonlinear part: >>>>>> >>>>>> mincresample -inverse_transformation -transformation >>>>>> nonLinTransformFileName.xfm -like nativeSpaceAnatomic.mnc >>>>>> templateSpaceSegmentedImage.mnc nativeSpaceSegmentedImage.mnc >>>>>> >>>>>> >>>>>> doesn't work whatever I do (reloading files or try simple variants >>>>>> of the >>>>>> command): >>>>>> >>>>>> Error: opening MINC file "./TMS_CON_44_nlfit_It_grid_0.mnc". >>>>>> input_transform: error reading transform. >>>>>> Error reading transformation file. >>>>>> >>>>>> >>>>>> Here is the content of nonLinTransformFileName.xfm: >>>>>> >>>>>> --------------------------------------------------------------------------------------------------- >>>>>> >>>>>> >>>>>> MNI Transform File >>>>>> %Sun Aug 5 12:30:27 2012>>> minctracc -clobber -nonlinear corrcoeff >>>>>> -weight >>>>>> 1 -stiffness 1 -similarity 0.3 -sub_lattice 6 -iterations 10 -step >>>>>> 4 4 4 >>>>>> -lattice_diam 12 12 12 -transformation >>>>>> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_4.xfm >>>>>> -source_mask >>>>>> >>>>>> /sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/mask/TMS_CON_44_skull_mask.mnc >>>>>> >>>>>> >>>>>> -model_mask >>>>>> >>>>>> /sb/home/prioux/tools/CIVET/Feb-2010-a/share/mni-models//icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc >>>>>> >>>>>> >>>>>> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_2_blur.mnc >>>>>> >>>>>> /tmp/best1stepnlreg.pl-UAIGq86o/Ticbm_avg_152_t1_tal_nlin_symmetric_VI_2_blur.mnc/sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/transforms/nonlinear/TMS_CON_44_nlfit_It.xfm >>>>>> >>>>>> >>>>>> %(Package mni_autoreg 0.99.3, compiled by >>>>>> tnguyen at localhost.localdomain >>>>>> (x86_64-unknown-linux-gnu) on Mon Aug 30 17:14:08 EDT 2010) >>>>>> >>>>>> Transform_Type = Linear; >>>>>> Linear_Transform = >>>>>> 1 0 0 0 >>>>>> 0 1 0 0 >>>>>> 0 0 1 0; >>>>>> Transform_Type = Grid_Transform; >>>>>> Displacement_Volume = TMS_CON_44_nlfit_It_grid_0.mnc; > > From sebastien.proulx2 at mcgill.ca Thu Jun 20 17:53:46 2013 From: sebastien.proulx2 at mcgill.ca (=?ISO-8859-1?Q?S=E9bastien_Proulx?=) Date: Thu, 20 Jun 2013 17:53:46 -0400 Subject: [MINC-users] mincresample apply nonlinear transformation using .xfm with Transform Type = Grid_Transform In-Reply-To: <17984_1371760914_51C36912_17984_62_1_51C368BA.9080404@bic.mni.mcgill.ca> References: <51C3434B.2030406@mcgill.ca> <51C35895.90703@mcgill.ca> <51C35FF8.6060003@mcgill.ca> <51C367AB.3080305@gmail.com> <17984_1371760914_51C36912_17984_62_1_51C368BA.9080404@bic.mni.mcgill.ca> Message-ID: <51C379EA.60806@mcgill.ca> Great! It runs now! although the segmented images these inverted transformations produce are somehow (significantly) not perfectly aligned to the original anatomical. I'll look at that later, maybe I don't have the good original anatomical, but at least the command runs!! Thanks a lot guys! S?bastien Proulx, MSc Research Assistant McGill University (514) 398-6644 #00445 Le 13-06-20 4:40 PM, Michael Ferreira a ?crit : > Hi Sebas, > > Since I see from your BIC home directory that you are a bash shell > user, type this: > > export PATH='/usr/local/bic/bin:'$PATH > > Then retry your mincresample command, it should work now. Your output > will be in MINC2 format though, so it may be wise to always use MINC2. > > To do this, add the above PATH definition to your ~/.bashrc file. This > way, every time you login to the BIC you will be using the MINC2 tools. > > Regards, > > mike > > > On 20/06/13 04:35 PM, Vladimir S. FONOV wrote: >> Hello, >> >> >> It looks like you received grid files in minc2 file format. And your >> computer (duncan) have minc1 installed. >> >> On 13-06-20 04:03 PM, S?bastien Proulx wrote: >>> It's not me who did the registration, I'm only trying to undo it :-P >>> (apply the inverse transform). My colleague gave me one subject, didn't >>> work. He sent it again along with another subject, didn't work either >>> for both. He could send me more, but I guess it would be the same. >>> >>> Same thing with min_cc_omplete. Trying stuff around, I copypasted the >>> wrong lines. >>> >>> As for the version: >>> duncan:~/transformTest_bis/Transforms_45/nonlinear> mincresample >>> -version >>> program: 1.5.1 >>> libminc: 1.5.1 >>> netcdf : "3.6.3" of May 20 2011 16:00:48 $ >>> >>> S?bastien Proulx, MSc >>> Research Assistant >>> McGill University >>> (514) 398-6644 #00445 >>> >>> Le 13-06-20 3:44 PM, Alex Zijdenbos a ?crit : >>>> 'minccomplete' has two 'c's :) >>>> >>>> you get the same error for all grid_0.mnc files, or just one? >>>> >>>> my other guess would be you are looking at a MINC1/MINC2 issue, and/or >>>> that you might have an ancient MINC install. What does 'mincresample >>>> -version' tell you? >>>> >>>> On Thu, Jun 20, 2013 at 3:31 PM, S?bastien Proulx >>>> wrote: >>>>> It seems like I don't have access to minccomplete, but see the >>>>> following >>>>> terminal output: >>>>> ------------------------------------------------------------------------------------- >>>>> >>>>> >>>>> >>>>> duncan:~/transformTest_bis/Transforms_45/nonlinear> mincomplete >>>>> TMS_CON_45_nlfit_It_grid_0.mnc >>>>> mincomplete: Command not found. >>>>> duncan:~/transformTest_bis/Transforms_45/nonlinear> mincinfo >>>>> TMS_CON_45_nlfit_It_grid_0.mnc >>>>> ncopen: filename "TMS_CON_45_nlfit_It_grid_0.mnc": NetCDF: Unknown >>>>> file >>>>> format >>>>> miopen: MINC package entry point >>>>> ------------------------------------------------------------------------------------- >>>>> >>>>> >>>>> >>>>> >>>>> Since I tried with two different subjects, I thought a corruption was >>>>> unlikely, but I guess mincinfo should be able to read any intact minc >>>>> file. >>>>> Is it possible that minctracc (see content of .xfm) did correctly >>>>> produce >>>>> the nonlinearly registered images, but somehow screwed-up all the >>>>> ..._nlfit_It_grid_0.mnc files? >>>>> >>>>> Thanks a lot Alex! >>>>> >>>>> >>>>> S?bastien Proulx, MSc >>>>> Research Assistant >>>>> McGill University >>>>> (514) 398-6644 #00445 >>>>> >>>>> Le 13-06-20 2:22 PM, Alex Zijdenbos a ?crit : >>>>>> Hi S?bastien, >>>>>> >>>>>> My guess would be that the deformation field (grid_0.mnc) file is >>>>>> corrupt. What happens when you run this: >>>>>> >>>>>> minccomplete TMS_CON_44_nlfit_It_grid_0.mnc >>>>>> >>>>>> and/or mincfinfo? >>>>>> >>>>>> -- A >>>>>> >>>>>> On Thu, Jun 20, 2013 at 2:00 PM, S?bastien Proulx >>>>>> wrote: >>>>>>> Hello Minc people, >>>>>>> >>>>>>> My colleague gave me transformation files from a nonlinear >>>>>>> registration >>>>>>> to a >>>>>>> template done with minctools. I'm trying to use those to bring some >>>>>>> images >>>>>>> (segmented in MNI space) back to their native space. Linear >>>>>>> transforms >>>>>>> are >>>>>>> working fine, but I apply the inverse of the nonlinear part: >>>>>>> >>>>>>> mincresample -inverse_transformation -transformation >>>>>>> nonLinTransformFileName.xfm -like nativeSpaceAnatomic.mnc >>>>>>> templateSpaceSegmentedImage.mnc nativeSpaceSegmentedImage.mnc >>>>>>> >>>>>>> >>>>>>> doesn't work whatever I do (reloading files or try simple variants >>>>>>> of the >>>>>>> command): >>>>>>> >>>>>>> Error: opening MINC file "./TMS_CON_44_nlfit_It_grid_0.mnc". >>>>>>> input_transform: error reading transform. >>>>>>> Error reading transformation file. >>>>>>> >>>>>>> >>>>>>> Here is the content of nonLinTransformFileName.xfm: >>>>>>> >>>>>>> --------------------------------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> >>>>>>> MNI Transform File >>>>>>> %Sun Aug 5 12:30:27 2012>>> minctracc -clobber -nonlinear corrcoeff >>>>>>> -weight >>>>>>> 1 -stiffness 1 -similarity 0.3 -sub_lattice 6 -iterations 10 -step >>>>>>> 4 4 4 >>>>>>> -lattice_diam 12 12 12 -transformation >>>>>>> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_4.xfm >>>>>>> -source_mask >>>>>>> >>>>>>> /sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/mask/TMS_CON_44_skull_mask.mnc >>>>>>> >>>>>>> >>>>>>> >>>>>>> -model_mask >>>>>>> >>>>>>> /sb/home/prioux/tools/CIVET/Feb-2010-a/share/mni-models//icbm_avg_152_t1_tal_nlin_symmetric_VI_mask.mnc >>>>>>> >>>>>>> >>>>>>> >>>>>>> /tmp/best1stepnlreg.pl-UAIGq86o/STMS_CON_44_t1_final_2_blur.mnc >>>>>>> >>>>>>> /tmp/best1stepnlreg.pl-UAIGq86o/Ticbm_avg_152_t1_tal_nlin_symmetric_VI_2_blur.mnc/sb/project/eim-670-ab/gridshare/15/52/01/stremblay-Civet-T155201/civet_out/CON_44/transforms/nonlinear/TMS_CON_44_nlfit_It.xfm >>>>>>> >>>>>>> >>>>>>> >>>>>>> %(Package mni_autoreg 0.99.3, compiled by >>>>>>> tnguyen at localhost.localdomain >>>>>>> (x86_64-unknown-linux-gnu) on Mon Aug 30 17:14:08 EDT 2010) >>>>>>> >>>>>>> Transform_Type = Linear; >>>>>>> Linear_Transform = >>>>>>> 1 0 0 0 >>>>>>> 0 1 0 0 >>>>>>> 0 0 1 0; >>>>>>> Transform_Type = Grid_Transform; >>>>>>> Displacement_Volume = TMS_CON_44_nlfit_It_grid_0.mnc; >> >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From sorench at gmail.com Tue Jun 25 18:12:01 2013 From: sorench at gmail.com (Soren Christensen) Date: Tue, 25 Jun 2013 15:12:01 -0700 Subject: [MINC-users] vessel registration to ICBM 152 Nonlinear atlases Message-ID: Hi, I would like to add a vessel tree (from a time of flight MRA for example) to the ICBM 152 Nonlinear atlas - the tree of a patient for use in simulations. Does anyone know of high resolution MRAs or CTAs freely available? Is it possible to register a patients TOF MRA to the ICBM 152 atlas? If so, what is the best tool to use for this - minctracc? Thanks Soren From a.janke at gmail.com Tue Jun 25 20:54:24 2013 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 26 Jun 2013 10:54:24 +1000 Subject: [MINC-users] vessel registration to ICBM 152 Nonlinear atlases In-Reply-To: References: Message-ID: Hi Soren, On 26 June 2013 08:12, Soren Christensen wrote: > Hi, > I would like to add a vessel tree (from a time of flight MRA for example) > to the ICBM 152 Nonlinear atlas - the tree of a patient for use in > simulations. > Does anyone know of high resolution MRAs or CTAs freely available? I don't know of any. > Is it possible to register a patients TOF MRA to the ICBM 152 atlas? If > so, what is the best tool to use for this - minctracc? I think you would be best to align the same subjects T1 image to the ICBM152 and apply this transformation to the MRA to get things started. a