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
