Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces
Thanks Doug, This does seem like it will do the right thing, but it’s failing because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to have an ico subject in my subjects_dir Should this normally be in the subjects_dir? I don’t recall ever seeing this made when I’ve run recon-all in the past. Thanks, Jared Here’s the full terminal output when I run the command: mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz --reg func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac 0.5 --interp trilinear --noreshape --trgsubject ico --icoorder 6 --out_type mgh --surf-fwhm 6 IcoOrder = 6, nIcoVtxs = 40962 srcvol = /func_test/filtered_func_residuals.nii.gz srcreg = func_test/coreg/fs_ep2struct_fsl.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = ico surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /subjdir_test//subID/surf/lh.white Done reading source surface Reading thickness /subjdir_test//subID/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 11345 Reading source surface registration subjdir_test//subID/surf/lh.sphere.reg Done loading source registration surface Reading icosahedron, order = 6, radius = 100 Reading icosahedron /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri Done loading target registration surface Mapping Surfaces (subID -> ico) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (40962) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (112745) Reverse Loop had 72236 hits > On Sep 28, 2016, at 3:34 PM, Douglas Greve wrote: > > You need to specify --trgsubject ico in mri_vol2surf > > > On 9/28/16 3:01 PM, Jared Zimmerman wrote: >> Hi All, forwarding this message along again as I'm still having some trouble >> getting this to work. Basically I would like to 1) project processed >> residual time-series from the subject-space volume to the subject-space >> surface, 2) smooth on the surface, 3) down-sample to FS4 space. >> >> To do this is have used bbregister to calculate the registration, then >> mri_vol2surf to project to the surface, but I am not sure the output of >> mri_vol2surf is what I should be expecting. The output file has dimensions >> 112745 x 1 x 1 x 120 when I'm expecting ~40k vertices for FS6 space and ~3k >> vertices for FS4 space, but changing the --icoorder flag seems to have no >> effect on the number of vertices in the output. >> >> I have loaded the output surface functional image into Matlab to se that >> there is real time-series data in there, but I have no way of knowing if it >> has mapped the data appropriately. Additionally, I've tried to use >> mri_surf2surf to downsample this data but have not ben able to successfully >> get that to downsample the surface. The mri_surf2surf call I used is as >> follows: >> >> mri_surf2surf --srcsubject subjID --srcsurfval >> /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh --trgsubject >> subjID --trgsurfval >> /mov_dir/filtered_func_residuals_fs4_lh_6mm_noreshape.mgh --hemi lh >> --trgicoorder 4 >> >> Any advice on how to achieve my goal of projecting to subject surfaces, >> smoothing and downsampling to FS4, as well as recommendations on how to >> visualize the surface functional data and confirm that the projections has >> worked properly would be much appreciated. Additionally, what should the >> dimensions of a surface time series look like? I would have expected for >> have an nVertices x nFrames x 1 array instead of the nVertices x 1 x 1 x >> nFrames array, is this correct? >> >> >> Thank you, >> Jared >> >> - Forwarded Message - >> From: "Jared Zimmerman" >> To: freesurfer@nmr.mgh.harvard.edu >> Sent: Monday, September 19, 2016 8:46:17 PM >> Subject: [Freesurfer] Projecting processed 4D functional data to individual >> surfaces >> >> Hi All, >> >> I'm trying to project some processed resting-state data onto the surface to >> run some surface based parcellations, and I'm running into a bit of >> difficulty. Basically I'm using bbregister to register my functional to the >> T1, then mri_vol2surf to project to the surface with the following >> pseudocode: >> >> bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \ >> --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \ >> --init-fsl --bold >> >> mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \ >> --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \ >> --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \ >> --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh --noreshape >> >> >> The registration looks pretty good after I run bbregister, but what I get >> out from the mri_
Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces
I want to project to the native subject surfaces though, not fsaverage. If I use —trgsubject subjID would that work with the —icoorder flag? Alternatively I guess I could project to fsaverage and then use mri_surf2surf to move back to the subject surface, but that seems like a roundabout way to do it and will probably add some unnecessary interpolation. Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder flags and I did successfully get output with 112745 vertices (is this FS7 space? I would have expected ~164k vertices, is this with medial wall masked?) and I could try to resample that with mri_surf2surf. I wasn’t able to do this before, but I didn’t use the flag —trgsubject or —trgicoorder flags, though I suspect I will run into the same problem trying doing this. I’m not at my computer now but can try this later this afternoon though. Thanks, Jared > On Sep 29, 2016, at 12:00 AM, Douglas Greve wrote: > > you can actually skip the ico thing and just use --trgsubject fsaverage6 > > On 9/28/16 7:06 PM, Jared P Zimmerman wrote: >> Thanks Doug, >> >> This does seem like it will do the right thing, but it’s failing because >> it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to have an ico subject >> in my subjects_dir >> >> Should this normally be in the subjects_dir? I don’t recall ever seeing >> this made when I’ve run recon-all in the past. >> >> Thanks, >> Jared >> >> Here’s the full terminal output when I run the command: >> >> mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz --reg >> func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o >> func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac 0.5 >> --interp trilinear --noreshape --trgsubject ico --icoorder 6 --out_type mgh >> --surf-fwhm 6 >> IcoOrder = 6, nIcoVtxs = 40962 >> srcvol = /func_test/filtered_func_residuals.nii.gz >> srcreg = func_test/coreg/fs_ep2struct_fsl.dat >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = lh >> trgsubject = ico >> surfreg = sphere.reg >> ProjFrac = 0.5 >> thickness = thickness >> reshape = 0 >> interp = trilinear >> float2int = round >> GetProjMax = 0 >> INFO: float2int code = 0 >> Done loading volume >> Reading surface /subjdir_test//subID/surf/lh.white >> Done reading source surface >> Reading thickness /subjdir_test//subID/surf/lh.thickness >> Done >> Mapping Source Volume onto Source Subject Surface >> 1 0.5 0.5 0.5 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 11345 >> Reading source surface registration >> subjdir_test//subID/surf/lh.sphere.reg >> Done loading source registration surface >> Reading icosahedron, order = 6, radius = 100 >>Reading icosahedron /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri >> Done loading target registration surface >> Mapping Surfaces (subID -> ico) >> surf2surf_nnfr: building source hash (res=16). >> Surf2Surf: Forward Loop (40962) >> >> surf2surf_nnfr: building target hash (res=16). >> Surf2Surf: Reverse Loop (112745) >> Reverse Loop had 72236 hits >> >>> On Sep 28, 2016, at 3:34 PM, Douglas Greve >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> You need to specify --trgsubject ico in mri_vol2surf >>> >>> >>> On 9/28/16 3:01 PM, Jared Zimmerman wrote: >>>> Hi All, forwarding this message along again as I'm still having some >>>> trouble getting this to work. Basically I would like to 1) project >>>> processed residual time-series from the subject-space volume to the >>>> subject-space surface, 2) smooth on the surface, 3) down-sample to FS4 >>>> space. >>>> >>>> To do this is have used bbregister to calculate the registration, then >>>> mri_vol2surf to project to the surface, but I am not sure the output of >>>> mri_vol2surf is what I should be expecting. The output file has >>>> dimensions 112745 x 1 x 1 x 120 when I'm expecting ~40k vertices for FS6 >>>> space and ~3k vertices for FS4 space, but changing the --icoorder flag >>>> seems to have no effect on the number of vertices in the output. >>>> >>>> I have loaded the output surface functional image into Matlab to se that >>>> there is real time-series data in there, but I have no way of knowing if >>>> it has mapped the data appropriately. Additionally, I've tried to use >>>> mri_surf2surf to downsample this data but ha
Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces
Ahh, thanks Bruce. Is there a way to downsample the subject meshes? -jared > On Sep 29, 2016, at 10:18 AM, Bruce Fischl wrote: > > Hi Jared > > the icosahedra are only used to represent average space surface > (fsaverage[4-7]), not individual subjects. > > cheers > Bruce > On Thu, 29 Sep 2016, Jared P Zimmerman wrote: > >> I want to project to the native subject surfaces though, not fsaverage. If >> I use —trgsubject subjID would that work with the —icoorder flag? >> Alternatively I guess I could project to fsaverage and then use >> mri_surf2surf to move back to the subject surface, but that seems like a >> roundabout way to do it and will probably add some unnecessary >> interpolation. >> Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder flags and >> I did successfully get output with 112745 vertices (is this FS7 space? I >> would have expected ~164k vertices, is this with medial wall masked?) and I >> could try to resample that with mri_surf2surf. I wasn’t able to do this >> before, but I didn’t use the flag —trgsubject or —trgicoorder flags, though >> I suspect I will run into the same problem trying doing this. I’m not at my >> computer now but can try this later this afternoon though. >> Thanks, >> Jared >> >> On Sep 29, 2016, at 12:00 AM, Douglas Greve >> wrote: >> you can actually skip the ico thing and just use --trgsubject >> fsaverage6 >> On 9/28/16 7:06 PM, Jared P Zimmerman wrote: >> Thanks Doug, >> This does seem like it will do the right thing, but it’s failing >> because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to >> have an ico subject in my subjects_dir >> Should this normally be in the subjects_dir? I don’t recall >> ever seeing this made when I’ve run recon-all in the past. >> Thanks, >> Jared >> Here’s the full terminal output when I run the command: >> mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz >> --reg func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o >> func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac >> 0.5 --interp trilinear --noreshape --trgsubject ico --icoorder 6 >> --out_type mgh --surf-fwhm 6 >> IcoOrder = 6, nIcoVtxs = 40962 >> srcvol = /func_test/filtered_func_residuals.nii.gz >> srcreg = func_test/coreg/fs_ep2struct_fsl.dat >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = lh >> trgsubject = ico >> surfreg = sphere.reg >> ProjFrac = 0.5 >> thickness = thickness >> reshape = 0 >> interp = trilinear >> float2int = round >> GetProjMax = 0 >> INFO: float2int code = 0 >> Done loading volume >> Reading surface /subjdir_test//subID/surf/lh.white >> Done reading source surface >> Reading thickness /subjdir_test//subID/surf/lh.thickness >> Done >> Mapping Source Volume onto Source Subject Surface >> 1 0.5 0.5 0.5 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 11345 >> Reading source surface registration >> subjdir_test//subID/surf/lh.sphere.reg >> Done loading source registration surface >> Reading icosahedron, order = 6, radius = 100 >> Reading icosahedron >> /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri >> Done loading target registration surface >> Mapping Surfaces (subID -> ico) >> surf2surf_nnfr: building source hash (res=16). >> Surf2Surf: Forward Loop (40962) >> surf2surf_nnfr: building target hash (res=16). >> Surf2Surf: Reverse Loop (112745) >> Reverse Loop had 72236 hits >> >> On Sep 28, 2016, at 3:34 PM, Douglas Greve >> wrote: >> You need to specify --trgsubject ico in mri_vol2surf >> On 9/28/16 3:01 PM, Jared Zimmerman wrote: >> Hi All, forwarding this message along again as >> I'm still having some trouble getting this to >> work. Basically I would like to 1) project >> processed residual time-series from the >> subject-space volume to the subject-space >> surface, 2) smooth on the surface, 3) >> down-sample to FS4 space. >> >> To do this is have used bbregister to >> calculate the registration, then mri_vol2surf >> to project to the surface, but I am not sure >> the output of mri_vol2surf is what I should be >> expecting. The output file has dimensions >> 112745 x 1 x 1 x 120 when I'm expecting ~40k >> vertices for FS6 space and ~3k vertices for >> FS4 space, but changing the --icoor
Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces
Yeah, I think I misunderstood what was happening with the ico registration. I thought it was using the ico to downsample the subject surface, but I see that this is an atlas space and I can do w/e calculations I need I this space and then register back to subject space after. Thanks for the help, I got it to work by doing mri_vol2surf to register to my subject surface and then mri_surf2surf to downsample. -jared > On Sep 29, 2016, at 12:34 PM, Douglas N Greve > wrote: > > I don't understand what you mean. When you use ico (when it used to > work), it always went to fsaverage space. Do you want to decimate the > native space surfaces? > > > On 09/29/2016 10:15 AM, Jared P Zimmerman wrote: >> I want to project to the native subject surfaces though, not >> fsaverage. If I use —trgsubject subjID would that work with the >> —icoorder flag? Alternatively I guess I could project to fsaverage >> and then use mri_surf2surf to move back to the subject surface, but >> that seems like a roundabout way to do it and will probably add some >> unnecessary interpolation. >> >> Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder >> flags and I did successfully get output with 112745 vertices (is this >> FS7 space? I would have expected ~164k vertices, is this with medial >> wall masked?) and I could try to resample that with mri_surf2surf. I >> wasn’t able to do this before, but I didn’t use the flag —trgsubject >> or —trgicoorder flags, though I suspect I will run into the same >> problem trying doing this. I’m not at my computer now but can try >> this later this afternoon though. >> >> Thanks, >> Jared >> >>> On Sep 29, 2016, at 12:00 AM, Douglas Greve >>> mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> >>> wrote: >>> >>> you can actually skip the ico thing and just use --trgsubject fsaverage6 >>> >>> >>> On 9/28/16 7:06 PM, Jared P Zimmerman wrote: >>>> Thanks Doug, >>>> >>>> This does seem like it will do the right thing, but it’s failing >>>> because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to >>>> have an ico subject in my subjects_dir >>>> >>>> Should this normally be in the subjects_dir? I don’t recall ever >>>> seeing this made when I’ve run recon-all in the past. >>>> >>>> Thanks, >>>> Jared >>>> >>>> Here’s the full terminal output when I run the command: >>>> >>>> mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz --reg >>>> func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o >>>> func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac 0.5 >>>> --interp trilinear --noreshape --trgsubject ico --icoorder 6 >>>> --out_type mgh --surf-fwhm 6 >>>> IcoOrder = 6, nIcoVtxs = 40962 >>>> srcvol = /func_test/filtered_func_residuals.nii.gz >>>> srcreg = func_test/coreg/fs_ep2struct_fsl.dat >>>> srcregold = 0 >>>> srcwarp unspecified >>>> surf = white >>>> hemi = lh >>>> trgsubject = ico >>>> surfreg = sphere.reg >>>> ProjFrac = 0.5 >>>> thickness = thickness >>>> reshape = 0 >>>> interp = trilinear >>>> float2int = round >>>> GetProjMax = 0 >>>> INFO: float2int code = 0 >>>> Done loading volume >>>> Reading surface /subjdir_test//subID/surf/lh.white >>>> Done reading source surface >>>> Reading thickness /subjdir_test//subID/surf/lh.thickness >>>> Done >>>> Mapping Source Volume onto Source Subject Surface >>>> 1 0.5 0.5 0.5 >>>> using old >>>> Done mapping volume to surface >>>> Number of source voxels hit = 11345 >>>> Reading source surface registration >>>> subjdir_test//subID/surf/lh.sphere.reg >>>> Done loading source registration surface >>>> Reading icosahedron, order = 6, radius = 100 >>>> Reading icosahedron /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri >>>> Done loading target registration surface >>>> Mapping Surfaces (subID -> ico) >>>> surf2surf_nnfr: building source hash (res=16). >>>> Surf2Surf: Forward Loop (40962) >>>> >>>> surf2surf_nnfr: building target hash (res=16). >>>> Surf2Surf: Reverse Loop (112745) >>>> Revers
[Freesurfer] error with mris_anatomical_stats OR mris_sample_parc
Hi FS Experts, I’m having trouble getting anatomical stats from a parcellation I made out of scanner-space volume ROIs. I have taken the following steps to do this. mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o myROI_orig.nii.gz --interp nearest mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct ROI_test_table.txt On this step I ALWAYS get an error “could not open translation file /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt” even though I specify a CT with -ct, or when I specify a table with -t, or with both This seems to work though and I can view this annot on the surface with tksurfer mris_anatomical_stats -a /path/to/myROIs.annot -b Subj111 lh When I run mris_anatomical_stats I get the following error: CTABfindAnnotation: ct was NULL Segmentation fault (core dumped) I’m guessing this is from the color-table not being embedded in the annot file, but I’ve tried to get that embedded in many ways. My questions are: What is causing the error with mris_anatomical_stats? What is the difference between the -t and -ct flags for mris_sample_parc and which should I use? Should I use a specific color-table for this? I made my own which was just a space delimited file with “index name r g b a” for all my ROIs, but should I be adding this data to some existing color-table to make this work? Thanks, Jared___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc
Any chance I could get some help on this? still having this problem > On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman > wrote: > > Hi FS Experts, > > I’m having trouble getting anatomical stats from a parcellation I made out of > scanner-space volume ROIs. I have taken the following steps to do this. > > mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o > myROI_orig.nii.gz --interp nearest > mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct > ROI_test_table.txt > On this step I ALWAYS get an error “could not open translation file > /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt” even though I > specify a CT with -ct, or when I specify a table with -t, or with both > This seems to work though and I can view this annot on the surface with > tksurfer > mris_anatomical_stats -a /path/to/myROIs.annot -b Subj111 lh > > > When I run mris_anatomical_stats I get the following error: > CTABfindAnnotation: ct was NULL > Segmentation fault (core dumped) > > I’m guessing this is from the color-table not being embedded in the annot > file, but I’ve tried to get that embedded in many ways. > > My questions are: > > What is causing the error with mris_anatomical_stats? > What is the difference between the -t and -ct flags for mris_sample_parc and > which should I use? > Should I use a specific color-table for this? I made my own which was just a > space delimited file with “index name r g b a” for all my ROIs, but should I > be adding this data to some existing color-table to make this work? > > Thanks, > Jared > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc
Here’s the script that I’m running and the merged stderr stdout. I’ve also tried various permutations of mris_sample_parc using the -t flag and using different LUTs than the one I made. Also copying the log here incase the text files get removed. Thanks, jared ./targetAnnotStats.sh: line 21: 4934 Segmentation fault (core dumped) mris_anatomical_stats -a ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot -b ${sub} lh >> log.txt 2>&1 reading parcellation volume from /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... reading input surface /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... could not open translation file /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt pass 1: 7 segments changed pass 2: 0 segments changed writing annotation to s111_bla_8mm_orig2_annot.annot... computing statistics for each annotation in /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/label/lh.s111_bla_8mm_orig2_annot.annot. reading volume /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/wm.mgz... reading input surface /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... reading input pial surface /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.pial... reading input white surface /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... CTABfindAnnotation: ct was NULL ./targetAnnotStats.sh: line 21: 5086 Segmentation fault (core dumped) mris_anatomical_stats -a ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot -b ${sub} lh ./targetAnnotStats.sh: line 21: 4934 Segmentation fault (core dumped) mris_anatomical_stats -a ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot -b ${sub} lh >> log.txt 2>&1 reading parcellation volume from /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... reading input surface /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... could not open translation file /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt pass 1: 7 segments changed pass 2: 0 segments changed writing annotation to s111_bla_8mm_orig2_annot.annot... computing statistics for each annotation in /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/label/lh.s111_bla_8mm_orig2_annot.annot. reading volume /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/wm.mgz... reading input surface /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... reading input pial surface /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.pial... reading input white surface /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... CTABfindAnnotation: ct was NULL ./targetAnnotStats.sh: line 21: 5086 Segmentation fault (core dumped) mris_anatomical_stats -a ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot -b ${sub} lh targetAnnotStats.sh Description: Binary data > On Apr 26, 2017, at 3:52 PM, Bruce Fischl wrote: > > Hi Jared > > can you send us the full command line and screen output? > > cheers > Bruce > On Wed, 26 Apr 2017, Jared P Zimmerman wrote: > >> Any chance I could get some help on this? still having this problem >> >> On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman >> wrote: >> Hi FS Experts, >> I’m having trouble getting anatomical stats from a parcellation I made >> out of scanner-space volume ROIs. I have taken the following steps to >> do this. >> >> 1. mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o >>myROI_orig.nii.gz --interp nearest >> 2. mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct >>ROI_test_table.txt >> 1. On this step I ALWAYS get an error “could not open translation >>file /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt” >>even though I specify a CT with -ct, or when I specify a table >>with -t, or with both >> 2. This seems to work though and I can view this annot on the >>surface with tksurfer >> 3. mris_anatomical_stats -a /path/to/myROIs.annot -b Subj111 lh >> When I run mris_anatomical_stats I get the following error: >> CTABfindAnnotation: ct was NULL >> Segmentation fault (core dumped) >> I’m guessing this is from the color-table not being embedded in the >> annot file, but I’ve tried to get that embedded in many ways. >> My questions are: >> >> 1. What is causing the error with mris_anatomical_stats? >> 2. What is the difference between the -t and -ct flags for >>mris_sample_parc and which should I use? >> 3. Should I use a specific color-table for this? I made my own which >>was just a space delimited file with “index name r g b a” for all >>my ROIs, but should I be adding this data to some existing >>
Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc
Hey Bruce et al, any update on this? Thanks, Jared > On Apr 28, 2017, at 2:48 PM, Jared P Zimmerman > wrote: > > Here’s the script that I’m running and the merged stderr stdout. I’ve also > tried various permutations of mris_sample_parc using the -t flag and using > different LUTs than the one I made. Also copying the log here incase the > text files get removed. > > Thanks, > jared > > > ./targetAnnotStats.sh: line 21: 4934 Segmentation fault (core dumped) > mris_anatomical_stats -a ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot > -b ${sub} lh >> log.txt 2>&1 > reading parcellation volume from > /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... > reading input surface > /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... > could not open translation file > /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt > pass 1: 7 segments changed > pass 2: 0 segments changed > writing annotation to s111_bla_8mm_orig2_annot.annot... > computing statistics for each annotation in > /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/label/lh.s111_bla_8mm_orig2_annot.annot. > reading volume > /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/wm.mgz... > reading input surface > /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... > reading input pial surface > /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.pial... > reading input white surface > /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... > CTABfindAnnotation: ct was NULL > ./targetAnnotStats.sh: line 21: 5086 Segmentation fault (core dumped) > mris_anatomical_stats -a ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot > -b ${sub} lh > > > > > > >> On Apr 26, 2017, at 3:52 PM, Bruce Fischl wrote: >> >> Hi Jared >> >> can you send us the full command line and screen output? >> >> cheers >> Bruce >> On Wed, 26 Apr 2017, Jared P Zimmerman wrote: >> >>> Any chance I could get some help on this? still having this problem >>> >>> On Apr 20, 2017, at 6:26 PM, Jared P Zimmerman >>> wrote: >>> Hi FS Experts, >>> I’m having trouble getting anatomical stats from a parcellation I made >>> out of scanner-space volume ROIs. I have taken the following steps to >>> do this. >>> >>> 1. mri_vol2vol --mov myROI.nii.gz --targ orig.mgz --regheader --o >>> myROI_orig.nii.gz --interp nearest >>> 2. mris_sample_parc Subj111 lh myROI_orig.nii.gz myROIs.annot -ct >>> ROI_test_table.txt >>>1. On this step I ALWAYS get an error “could not open translation >>> file /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt” >>> even though I specify a CT with -ct, or when I specify a table >>> with -t, or with both >>>2. This seems to work though and I can view this annot on the >>> surface with tksurfer >>> 3. mris_anatomical_stats -a /path/to/myROIs.annot -b Subj111 lh >>> When I run mris_anatomical_stats I get the following error: >>> CTABfindAnnotation: ct was NULL >>> Segmentation fault (core dumped) >>> I’m guessing this is from the color-table not being embedded in the >>> annot file, but I’ve tried to get that embedded in many ways. >>> My questions are: >>> >>> 1. What is causing the error with mris_anatomical_stats? >>> 2. What is the difference between the -t and -ct flags for >>> mris_sample_parc and which should I use? >>> 3. Should I use a specific color-table for this? I made my own which >>> was just a space delimited file with “index name r g b a” for all >>> my ROIs, but should I be adding this data to some existing >>> color-table to make this work? >>> Thanks, >>> Jared >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender >>> and properly >
Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc
That’s what I did below, see the script and log.txt attached to a previous email. This is the output from the mris_sample_parc step >>>>> reading parcellation volume from >>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... >>>>> reading input surface >>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>>> could not open translation file >>>>> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt >>>>> pass 1: 7 segments changed >>>>> pass 2: 0 segments changed >>>>> writing annotation to s111_bla_8mm_orig2_annot.annot… Thanks, Jared > On May 4, 2017, at 11:36 AM, Bruce Fischl wrote: > > can you try it with -ct > > and send us the output if that doesn't work? That's what we use internally > cheers > Bruce > On Thu, 4 May 2017, Jared P Zimmerman wrote: > >> Yeah I see that, but the cma_parcellation_colors.txt isn’t distributed with >> FS 5.3, yet it is the default LUT called by mris_sample_parc. Also, I tried >> to use my own color table using the -ct flag but it continues to try to >> embed the cma_parcellation_colors.txt regardless of the LUT I put there. >> >> Also, mris_sample_parc seems to work. I can visualize the parcellation that >> comes out of that fine, however it’s clear there’s no LUT embedded because >> the label names are wrong (see attached image). >> >> I don’t care too much if the LUT is embedded properly, I just want to use >> the parcellation to get anatomical data about my regions, but >> mris_anatomical_stats seems to fail because the LUT isn’t embedded. I’m >> still confused about why the -ct flag in mris_sample_parc doesn’t seem to >> work. >> >> >> Thanks, >> Jared >> >> >> >> >>> On May 4, 2017, at 10:58 AM, Bruce Fischl >>> wrote: >>> >>> Hi Jared >>> >>> it looks like it couldn't find the lookup tbale: >>> >>>> reading input surface >>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>> could not open translation file >>> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt >>> >>> >>> cheers >>> Bruce >>> On Thu, 4 May 2017, Jared P Zimmerman wrote: >>> >>>> Hey Bruce et al, any update on this? >>>> >>>> >>>> Thanks, >>>> Jared >>>> >>>>> On Apr 28, 2017, at 2:48 PM, Jared P Zimmerman >>>>> wrote: >>>>> >>>>> Here’s the script that I’m running and the merged stderr stdout. I’ve >>>>> also tried various permutations of mris_sample_parc using the -t flag and >>>>> using different LUTs than the one I made. Also copying the log here >>>>> incase the text files get removed. >>>>> >>>>> Thanks, >>>>> jared >>>>> >>>>> >>>>> ./targetAnnotStats.sh: line 21: 4934 Segmentation fault (core >>>>> dumped) mris_anatomical_stats -a >>>>> ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot -b ${sub} lh >> >>>>> log.txt 2>&1 >>>>> reading parcellation volume from >>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... >>>>> reading input surface >>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>>> could not open translation file >>>>> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt >>>>> pass 1: 7 segments changed >>>>> pass 2: 0 segments changed >>>>> writing annotation to s111_bla_8mm_orig2_annot.annot... >>>>> computing statistics for each annotation in >>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/label/lh.s111_bla_8mm_orig2_annot.annot. >>>>> reading volume >>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/wm.mgz... >>>>> reading input surface >>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>>> reading input pial surface >>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.pial... >>>>> reading input white surface >>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>>> CTABfindAnnotation: ct was NULL &g
Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc
fwiw, this problem persists in FS6.0 -jared > On May 4, 2017, at 12:11 PM, Jared P Zimmerman > wrote: > > That’s what I did below, see the script and log.txt attached to a previous > email. This is the output from the mris_sample_parc step > >>>>>> reading parcellation volume from >>>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... >>>>>> reading input surface >>>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>>>> could not open translation file >>>>>> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt >>>>>> pass 1: 7 segments changed >>>>>> pass 2: 0 segments changed >>>>>> writing annotation to s111_bla_8mm_orig2_annot.annot… > > Thanks, > Jared > > > >> On May 4, 2017, at 11:36 AM, Bruce Fischl wrote: >> >> can you try it with -ct >> >> and send us the output if that doesn't work? That's what we use internally >> cheers >> Bruce >> On Thu, 4 May 2017, Jared P Zimmerman wrote: >> >>> Yeah I see that, but the cma_parcellation_colors.txt isn’t distributed with >>> FS 5.3, yet it is the default LUT called by mris_sample_parc. Also, I >>> tried to use my own color table using the -ct flag but it continues to try >>> to embed the cma_parcellation_colors.txt regardless of the LUT I put there. >>> >>> Also, mris_sample_parc seems to work. I can visualize the parcellation >>> that comes out of that fine, however it’s clear there’s no LUT embedded >>> because the label names are wrong (see attached image). >>> >>> I don’t care too much if the LUT is embedded properly, I just want to use >>> the parcellation to get anatomical data about my regions, but >>> mris_anatomical_stats seems to fail because the LUT isn’t embedded. I’m >>> still confused about why the -ct flag in mris_sample_parc doesn’t seem to >>> work. >>> >>> >>> Thanks, >>> Jared >>> >>> >>> >>> >>>> On May 4, 2017, at 10:58 AM, Bruce Fischl >>>> wrote: >>>> >>>> Hi Jared >>>> >>>> it looks like it couldn't find the lookup tbale: >>>> >>>>> reading input surface >>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>>> could not open translation file >>>> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt >>>> >>>> >>>> cheers >>>> Bruce >>>> On Thu, 4 May 2017, Jared P Zimmerman wrote: >>>> >>>>> Hey Bruce et al, any update on this? >>>>> >>>>> >>>>> Thanks, >>>>> Jared >>>>> >>>>>> On Apr 28, 2017, at 2:48 PM, Jared P Zimmerman >>>>>> wrote: >>>>>> >>>>>> Here’s the script that I’m running and the merged stderr stdout. I’ve >>>>>> also tried various permutations of mris_sample_parc using the -t flag >>>>>> and using different LUTs than the one I made. Also copying the log here >>>>>> incase the text files get removed. >>>>>> >>>>>> Thanks, >>>>>> jared >>>>>> >>>>>> >>>>>> ./targetAnnotStats.sh: line 21: 4934 Segmentation fault (core >>>>>> dumped) mris_anatomical_stats -a >>>>>> ${SUBJECTS_DIR}/${sub}/label/lh.${targ}_annot.annot -b ${sub} lh >> >>>>>> log.txt 2>&1 >>>>>> reading parcellation volume from >>>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... >>>>>> reading input surface >>>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>>>> could not open translation file >>>>>> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt >>>>>> pass 1: 7 segments changed >>>>>> pass 2: 0 segments changed >>>>>> writing annotation to s111_bla_8mm_orig2_annot.annot... >>>>>> computing statistics for each annotation in >>>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/label/lh.s111_bla_8mm_orig2_annot.annot. >>>>>> reading volume >>>>>&g
Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc
mris_sample_parc ${sub} \ lh ${targ}.nii.gz \ ${targ}_fs6_annot.annot \ -ct ${SUBJECTS_DIR}/${sub}/bla_test_table.txt This is the call from my script, which didn’t get written to stdout. The bla_test_table.txt exists, and is just a space delimited file with “index name r g b a” for each label. I’ve also tried pointing the -ct flag to a LUT that exists in $FREESURFER_HOME and is distributed with FS, e.g. ASegStatsLUT.txt or FreeSurferColorLUT.txt with no success, i.e. below. > mris_sample_parc Subj111 lh s111_bla_8mm_orig2.nii.gz > s111_bla_8mm_orig2_v2_annot.annot -ct AsegStatsLUT.txt > reading parcellation volume from > /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... > reading input surface > /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... > pass 1: 7 segments changed > pass 2: 0 segments changed > could not open translation file > /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt > writing annotation to s111_bla_8mm_orig2_v2_annot.annot… Thanks, Jared > On May 4, 2017, at 12:15 PM, Bruce Fischl wrote: > > sorry, I don't see the mris_sample_parc command line. Can you just send it > and the entire screen output? > On Thu, 4 May 2017, Jared P Zimmerman wrote: > >> That’s what I did below, see the script and log.txt attached to a previous >> email. This is the output from the mris_sample_parc step >> >>>>>>> reading parcellation volume from >>>>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... >>>>>>> reading input surface >>>>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>>>>> could not open translation file >>>>>>> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt >>>>>>> pass 1: 7 segments changed >>>>>>> pass 2: 0 segments changed >>>>>>> writing annotation to s111_bla_8mm_orig2_annot.annot… >> >> Thanks, >> Jared >> >> >> >>> On May 4, 2017, at 11:36 AM, Bruce Fischl >>> wrote: >>> >>> can you try it with -ct >>> >>> and send us the output if that doesn't work? That's what we use internally >>> cheers >>> Bruce >>> On Thu, 4 May 2017, Jared P Zimmerman wrote: >>> >>>> Yeah I see that, but the cma_parcellation_colors.txt isn’t distributed >>>> with FS 5.3, yet it is the default LUT called by mris_sample_parc. Also, >>>> I tried to use my own color table using the -ct flag but it continues to >>>> try to embed the cma_parcellation_colors.txt regardless of the LUT I put >>>> there. >>>> >>>> Also, mris_sample_parc seems to work. I can visualize the parcellation >>>> that comes out of that fine, however it’s clear there’s no LUT embedded >>>> because the label names are wrong (see attached image). >>>> >>>> I don’t care too much if the LUT is embedded properly, I just want to use >>>> the parcellation to get anatomical data about my regions, but >>>> mris_anatomical_stats seems to fail because the LUT isn’t embedded. I’m >>>> still confused about why the -ct flag in mris_sample_parc doesn’t seem to >>>> work. >>>> >>>> >>>> Thanks, >>>> Jared >>>> >>>> >>>> >>>> >>>>> On May 4, 2017, at 10:58 AM, Bruce Fischl >>>>> wrote: >>>>> >>>>> Hi Jared >>>>> >>>>> it looks like it couldn't find the lookup tbale: >>>>> >>>>>> reading input surface >>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>>>> could not open translation file >>>>> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt >>>>> >>>>> >>>>> cheers >>>>> Bruce >>>>> On Thu, 4 May 2017, Jared P Zimmerman wrote: >>>>> >>>>>> Hey Bruce et al, any update on this? >>>>>> >>>>>> >>>>>> Thanks, >>>>>> Jared >>>>>> >>>>>>> On Apr 28, 2017, at 2:48 PM, Jared P Zimmerman >>>>>>> wrote: >>>>>>> >>>>>>> Here’s the script that I’m running and the merged stderr stdout. I’ve >>>>>
Re: [Freesurfer] error with mris_anatomical_stats OR mris_sample_parc
Thanks Bruce, this did it. -jared > On May 4, 2017, at 12:33 PM, Bruce Fischl wrote: > > I see. This is the problem - mris_sample_parc is one of the binaries that > requires all options come before the mandatory arguments. Move the -ct > part to the beginning and it should work > > cheers > Bruce > On Thu, 4 May 2017, Jared P Zimmerman wrote: > >> mris_sample_parc ${sub} \ >> lh ${targ}.nii.gz \ >> ${targ}_fs6_annot.annot \ >> -ct ${SUBJECTS_DIR}/${sub}/bla_test_table.txt >> >> >> This is the call from my script, which didn’t get written to stdout. The >> bla_test_table.txt exists, and is just a space delimited file with “index >> name r g b a” for each label. I’ve also tried pointing the -ct flag to a >> LUT that exists in $FREESURFER_HOME and is distributed with FS, e.g. >> ASegStatsLUT.txt or FreeSurferColorLUT.txt with no success, i.e. below. >> >>> mris_sample_parc Subj111 lh s111_bla_8mm_orig2.nii.gz >>> s111_bla_8mm_orig2_v2_annot.annot -ct AsegStatsLUT.txt >>> reading parcellation volume from >>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... >>> reading input surface >>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>> pass 1: 7 segments changed >>> pass 2: 0 segments changed >>> could not open translation file >>> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt >>> writing annotation to s111_bla_8mm_orig2_v2_annot.annot… >> >> Thanks, >> Jared >> >> >>> On May 4, 2017, at 12:15 PM, Bruce Fischl >>> wrote: >>> >>> sorry, I don't see the mris_sample_parc command line. Can you just send it >>> and the entire screen output? >>> On Thu, 4 May 2017, Jared P Zimmerman wrote: >>> >>>> That’s what I did below, see the script and log.txt attached to a previous >>>> email. This is the output from the mris_sample_parc step >>>> >>>>>>>>> reading parcellation volume from >>>>>>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/mri/s111_bla_8mm_orig2.nii.gz... >>>>>>>>> reading input surface >>>>>>>>> /data/jag/cnds/seda/TMSfMRI_T1s/freesurfer/Subj111/surf/lh.white... >>>>>>>>> could not open translation file >>>>>>>>> /share/apps/freesurfer/5.3.0/cma_parcellation_colors.txt >>>>>>>>> pass 1: 7 segments changed >>>>>>>>> pass 2: 0 segments changed >>>>>>>>> writing annotation to s111_bla_8mm_orig2_annot.annot… >>>> >>>> Thanks, >>>> Jared >>>> >>>> >>>> >>>>> On May 4, 2017, at 11:36 AM, Bruce Fischl >>>>> wrote: >>>>> >>>>> can you try it with -ct >>>>> >>>>> and send us the output if that doesn't work? That's what we use internally >>>>> cheers >>>>> Bruce >>>>> On Thu, 4 May 2017, Jared P Zimmerman wrote: >>>>> >>>>>> Yeah I see that, but the cma_parcellation_colors.txt isn’t distributed >>>>>> with FS 5.3, yet it is the default LUT called by mris_sample_parc. >>>>>> Also, I tried to use my own color table using the -ct flag but it >>>>>> continues to try to embed the cma_parcellation_colors.txt regardless of >>>>>> the LUT I put there. >>>>>> >>>>>> Also, mris_sample_parc seems to work. I can visualize the parcellation >>>>>> that comes out of that fine, however it’s clear there’s no LUT embedded >>>>>> because the label names are wrong (see attached image). >>>>>> >>>>>> I don’t care too much if the LUT is embedded properly, I just want to >>>>>> use the parcellation to get anatomical data about my regions, but >>>>>> mris_anatomical_stats seems to fail because the LUT isn’t embedded. I’m >>>>>> still confused about why the -ct flag in mris_sample_parc doesn’t seem >>>>>> to work. >>>>>> >>>>>> >>>>>> Thanks, >>>>>> Jared >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> On May 4, 2017, at 10:58 AM, Bruce Fischl >>>&g