Freesurfer July 2008

freesurfer@nmr.mgh.harvard.edu

55 participants
74 discussions

Screening specific subcortical structures in large samples
by Nicolas Cherbuin 29 Jul '08

29 Jul '08

Hi, I need to check the segmentation of a number of subcortical structures in a large sample. Is there a simple way to automatically display in a grid, say the segmented putamen of all subjects in one directory? Or alternatively to produce a picture file for this structure from a specific view point for all subjects which then could be quickly scanned for defects? I have used Slicer to view single structures in 3D and while it works very well it is too slow to look at many structures in hundreds of subjects.... Thanks for your help Nic

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How to do F test in fsfast?
by Zhen Zonglei 29 Jul '08

29 Jul '08

Dear fs/fsfast user: Would you please tell me how to do F test in fsfast? For example, I have 4 conditions, and want to test the 4x4 contrast matrix [1 0 0 0; 0 1 0 0; 0 0 1 0;0 0 0 1] with a F test. How should I use mkcontrast-sess or other commands to construct the contrast matrix and do F test? Thanks in advance. -- Zonglei Zhen, Ph.D Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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ASEG atlas modality
by Mishkin Derakhshan 28 Jul '08

28 Jul '08

Hi, >From what I read here: https://surfer.nmr.mgh.harvard.edu/fswiki/AsegOptimization The atlas has is made from 27 data sets (14 GE, 13 SIEMENS). Can you give a bit more info about the sequences used. ie were they FLASH-based or MPRAGE. Are these 27 data sets available for download somewhere? thanks, mishkin

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Re: [Freesurfer] AFNI /freesurfer aseg files problem
by Liat Levita 28 Jul '08

28 Jul '08

Hi Doug, I just checked, yes they are. Liat PS. I attached the Info files to this message. ----- Original Message ----- From: Doug Greve <greve(a)nmr.mgh.harvard.edu> Date: Monday, July 28, 2008 12:16 pm Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem > are you sure that t1rc and pscA are the same dimension? Remember, > freesurfer resamples everything into 1mm3, 256^3 > > doug > > > > Liat Levita wrote: > > >Hello, > >I wonder if anyone using AFNI converted freesurfer files has come > across this problem (or can tell me if I making an error somewhere > that I am just not seeing right now). I posted the same question on > the AFNI board but haven't gotten feedback as yet. > > > >Here is the problem: > > > >After using freesurfer to get subcortical segmentations, I > converted the resulting freesurfer files to AFNI format, which was > fine - I had no problems doing that. However, when I try use these > subcortical segmentation data files (subjectID_aseg_m_at3+tlrc) as > masks to pull put PSC signal from each region of interest, I am > getting an odd effect of right versus left; whereby left clusters > output is fine ( voxel numbers are correct after 3dmaskave), but > for the left it is very wrong. I have checked that the labels of > the ROIs I am using are correct on AFNI GUI and they are. (code and > output below) > > > >I am a bit at a loss; any help will be much appreciated. > > > >Liat > > > >AFNI Code used > >--------------- > >Foreach subj (xxx) > >foreach cluster (18 54) > >3dmaskave -q -mask ${subj}_aseg_m_at3+tlrc -mrange ${cluster} > ${cluster} \ > >"${subj}_all_runs_pscA_at3+tlrc" > > ${subj}_fsROI_PSC_cluster_${cluster}.1D > >end > >end > > > >Output (get the same odd voxel output from all right hand side of > the brain freesurfer generated ROIs) > >------------------- > >*For cluster 18 Left Amygdala > >++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit] > >+++ 37 voxels survive the mask > > > >*For cluster 54 Right Amygdala > >++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit] > >+++ 200 voxels survive the mask > > > > > > > > > >_______________________________________________ > >Freesurfer mailing list > >Freesurfer(a)nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] AFNI /freesurfer aseg files problem
by Liat Levita 28 Jul '08

28 Jul '08

Thank you Doug. I also just got help from the AFNI message board which solved the problem: so here is a note for AFNI/freesurfer users if they come across this too - if you run AFNI's @auto_tlrc command use the '-rmode NN' so that it does nearest neighbor resampling. ----- Original Message ----- From: Doug Greve <greve(a)nmr.mgh.harvard.edu> Date: Monday, July 28, 2008 1:37 pm Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem > Sorry, don't know anything about those commands. You're probably > better > off registering the functional data directly to the anatomical > (fslregister or spmregister) rather than going thru the talairach > transform. You can then use mri_vol2vol to map the functional to > the > anatomical, then mri_segstats to exctract the average functional > value > (or you can probably use the afni command at that point). > > doug > > Liat Levita wrote: > > >Hello Doug, > >I transformed the aseg_m file to be 3x3x3. > >I will try and trouble shot the possible error in that transform- > > > >The AFNI steps I used to transform the freesurfer files to AFNI > format, and than to be 3x3x3 are pasted below. > > > >Liat > > > >----- > >foreach subj (xxx) > > > > > >#step1 > >@SUMA_Make_Spec_FS -sid ${subj} > > > >#step2 > > > >@SUMA_AlignToExperiment \ > >-exp_anat > /Volumes/cbgb/Liat/freesurfer_subjects/${subj}/SUMA/${subj}_anat+orig \ > >-surf_anat > /Volumes/cbgb/Liat/freesurfer_subjects/${subj}/SUMA/${subj}_SurfVol+orig \ > >-wd \ > >-prefix ${subj}_AlignExp > > > > > >#step 3: To align a given parcellation file > > > >3dWarp -NN -matparent ${subj}_AlignExp+orig -prefix ${subj}_aseg_m > aseg.nii> > >#step 4: I transformed the functional data set by the talairch > transform obtained for the anatomical data, and then which was > resampled to a 3x3x3 space during this step. > > > >@auto_tlrc -apar ${subj}_anat_at+tlrc -input > ${subj}_FC_Seed_aseg_fs_AMY_stats_ni_pi_Final+orig -dxyz 3 -suffix > _at3> > >end > > > > > > > > > > > >----- Original Message ----- > >From: Doug Greve <greve(a)nmr.mgh.harvard.edu> > >Date: Monday, July 28, 2008 1:07 pm > >Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem > > > > > > > >>I would suspect that something happened when you converted to > afni > >>format. The aseg starts out at 1mm3, 256^3, but it appears to be > >>3mm3, > >>54x64x50. These conversions are quit tricky and easy to get > wrong. > >>Also, > >>did you check the aseg.stats file to assure that the volumes of > the > >>amyg > >>are more-or-less symetrical? > >> > >>doug > >> > >> > >>R-to-L extent: -79.500 [R] -to- 79.500 [L] -step- 3.000 > mm > >>[ 54 > >>voxels] > >>A-to-P extent: -79.500 [A] -to- 109.500 [P] -step- 3.000 > mm > >>[ 64 > >>voxels] > >>I-to-S extent: -63.500 [I] -to- 83.500 [S] -step- 3.000 > mm > >>[ 50 > >>voxels] > >> > >> > >>Liat Levita wrote: > >> > >> > >> > >>>Hi Doug, I just checked, yes they are. > >>> > >>>Liat > >>> > >>>PS. I attached the Info files to this message. > >>> > >>> > >>> > >>> > >>>----- Original Message ----- > >>>From: Doug Greve <greve(a)nmr.mgh.harvard.edu> > >>>Date: Monday, July 28, 2008 12:16 pm > >>>Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem > >>> > >>> > >>> > >>> > >>> > >>>>are you sure that t1rc and pscA are the same dimension? > Remember, > >>>>freesurfer resamples everything into 1mm3, 256^3 > >>>> > >>>>doug > >>>> > >>>> > >>>> > >>>>Liat Levita wrote: > >>>> > >>>> > >>>> > >>>> > >>>> > >>>>>Hello, > >>>>>I wonder if anyone using AFNI converted freesurfer files has > >>>>> > >>>>> > >>come > >> > >> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>across this problem (or can tell me if I making an error > >>>> > >>>> > >>somewhere > >> > >> > >>>>that I am just not seeing right now). I posted the same > question > >>>> > >>>> > >>on > >> > >> > >>>>the AFNI board but haven't gotten feedback as yet. > >>>> > >>>> > >>>> > >>>> > >>>>>Here is the problem: > >>>>> > >>>>>After using freesurfer to get subcortical segmentations, I > >>>>> > >>>>> > >>>>> > >>>>> > >>>>converted the resulting freesurfer files to AFNI format, which > >>>> > >>>> > >>was > >> > >> > >>>>fine - I had no problems doing that. However, when I try use > >>>> > >>>> > >>these > >> > >> > >>>>subcortical segmentation data files (subjectID_aseg_m_at3+tlrc) > >>>> > >>>> > >>as > >> > >> > >>>>masks to pull put PSC signal from each region of interest, I am > >>>>getting an odd effect of right versus left; whereby left > clusters > >>>>output is fine ( voxel numbers are correct after 3dmaskave), > but > >>>>for the left it is very wrong. I have checked that the labels > of > >>>>the ROIs I am using are correct on AFNI GUI and they are. (code > >>>> > >>>> > >>and > >> > >> > >>>>output below) > >>>> > >>>> > >>>> > >>>> > >>>>>I am a bit at a loss; any help will be much appreciated. > >>>>> > >>>>>Liat > >>>>> > >>>>>AFNI Code used > >>>>>--------------- > >>>>>Foreach subj (xxx) > >>>>>foreach cluster (18 54) > >>>>>3dmaskave -q -mask ${subj}_aseg_m_at3+tlrc -mrange ${cluster} > >>>>> > >>>>> > >>>>> > >>>>> > >>>>${cluster} \ > >>>> > >>>> > >>>> > >>>> > >>>>>"${subj}_all_runs_pscA_at3+tlrc" > > >>>>> > >>>>> > >>>>> > >>>>> > >>>>${subj}_fsROI_PSC_cluster_${cluster}.1D > >>>> > >>>> > >>>> > >>>> > >>>>>end > >>>>>end > >>>>> > >>>>>Output (get the same odd voxel output from all right hand side > >>>>> > >>>>> > >>of > >> > >> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>the brain freesurfer generated ROIs) > >>>> > >>>> > >>>> > >>>> > >>>>>------------------- > >>>>>*For cluster 18 Left Amygdala > >>>>>++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) > [32- > >>>>> > >>>>> > >>bit]>>>+++ 37 voxels survive the mask > >> > >> > >>>>>*For cluster 54 Right Amygdala > >>>>>++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) > [32- > >>>>> > >>>>> > >>bit]>>>+++ 200 voxels survive the mask > >> > >> > >>>>> > >>>>> > >>>>>_______________________________________________ > >>>>>Freesurfer mailing list > >>>>>Freesurfer(a)nmr.mgh.harvard.edu > >>>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>-- > >>>>Douglas N. Greve, Ph.D. > >>>>MGH-NMR Center > >>>>greve(a)nmr.mgh.harvard.edu > >>>>Phone Number: 617-724-2358 > >>>>Fax: 617-726-7422 > >>>> > >>>>In order to help us help you, please follow the steps in: > >>>>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>>> > >>>> > >>>>_______________________________________________ > >>>>Freesurfer mailing list > >>>>Freesurfer(a)nmr.mgh.harvard.edu > >>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> > >>>> > >>>> > >>-- > >>Douglas N. Greve, Ph.D. > >>MGH-NMR Center > >>greve(a)nmr.mgh.harvard.edu > >>Phone Number: 617-724-2358 > >>Fax: 617-726-7422 > >> > >>In order to help us help you, please follow the steps in: > >>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > >> > >> > >> > >> > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >

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Re: [Freesurfer] AFNI /freesurfer aseg files problem
by Liat Levita 28 Jul '08

28 Jul '08

Hello Doug, I transformed the aseg_m file to be 3x3x3. I will try and trouble shot the possible error in that transform- The AFNI steps I used to transform the freesurfer files to AFNI format, and than to be 3x3x3 are pasted below. Liat ----- foreach subj (xxx) #step1 @SUMA_Make_Spec_FS -sid ${subj} #step2 @SUMA_AlignToExperiment \ -exp_anat /Volumes/cbgb/Liat/freesurfer_subjects/${subj}/SUMA/${subj}_anat+orig \ -surf_anat /Volumes/cbgb/Liat/freesurfer_subjects/${subj}/SUMA/${subj}_SurfVol+orig \ -wd \ -prefix ${subj}_AlignExp #step 3: To align a given parcellation file 3dWarp -NN -matparent ${subj}_AlignExp+orig -prefix ${subj}_aseg_m aseg.nii #step 4: I transformed the functional data set by the talairch transform obtained for the anatomical data, and then which was resampled to a 3x3x3 space during this step. @auto_tlrc -apar ${subj}_anat_at+tlrc -input ${subj}_FC_Seed_aseg_fs_AMY_stats_ni_pi_Final+orig -dxyz 3 -suffix _at3 end ----- Original Message ----- From: Doug Greve <greve(a)nmr.mgh.harvard.edu> Date: Monday, July 28, 2008 1:07 pm Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem > > I would suspect that something happened when you converted to afni > format. The aseg starts out at 1mm3, 256^3, but it appears to be > 3mm3, > 54x64x50. These conversions are quit tricky and easy to get wrong. > Also, > did you check the aseg.stats file to assure that the volumes of the > amyg > are more-or-less symetrical? > > doug > > > R-to-L extent: -79.500 [R] -to- 79.500 [L] -step- 3.000 mm > [ 54 > voxels] > A-to-P extent: -79.500 [A] -to- 109.500 [P] -step- 3.000 mm > [ 64 > voxels] > I-to-S extent: -63.500 [I] -to- 83.500 [S] -step- 3.000 mm > [ 50 > voxels] > > > Liat Levita wrote: > > >Hi Doug, I just checked, yes they are. > > > >Liat > > > >PS. I attached the Info files to this message. > > > > > > > > > >----- Original Message ----- > >From: Doug Greve <greve(a)nmr.mgh.harvard.edu> > >Date: Monday, July 28, 2008 12:16 pm > >Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem > > > > > > > >>are you sure that t1rc and pscA are the same dimension? Remember, > >>freesurfer resamples everything into 1mm3, 256^3 > >> > >>doug > >> > >> > >> > >>Liat Levita wrote: > >> > >> > >> > >>>Hello, > >>>I wonder if anyone using AFNI converted freesurfer files has > come > >>> > >>> > >>across this problem (or can tell me if I making an error > somewhere > >>that I am just not seeing right now). I posted the same question > on > >>the AFNI board but haven't gotten feedback as yet. > >> > >> > >>>Here is the problem: > >>> > >>>After using freesurfer to get subcortical segmentations, I > >>> > >>> > >>converted the resulting freesurfer files to AFNI format, which > was > >>fine - I had no problems doing that. However, when I try use > these > >>subcortical segmentation data files (subjectID_aseg_m_at3+tlrc) > as > >>masks to pull put PSC signal from each region of interest, I am > >>getting an odd effect of right versus left; whereby left clusters > >>output is fine ( voxel numbers are correct after 3dmaskave), but > >>for the left it is very wrong. I have checked that the labels of > >>the ROIs I am using are correct on AFNI GUI and they are. (code > and > >>output below) > >> > >> > >>>I am a bit at a loss; any help will be much appreciated. > >>> > >>>Liat > >>> > >>>AFNI Code used > >>>--------------- > >>>Foreach subj (xxx) > >>>foreach cluster (18 54) > >>>3dmaskave -q -mask ${subj}_aseg_m_at3+tlrc -mrange ${cluster} > >>> > >>> > >>${cluster} \ > >> > >> > >>>"${subj}_all_runs_pscA_at3+tlrc" > > >>> > >>> > >>${subj}_fsROI_PSC_cluster_${cluster}.1D > >> > >> > >>>end > >>>end > >>> > >>>Output (get the same odd voxel output from all right hand side > of > >>> > >>> > >>the brain freesurfer generated ROIs) > >> > >> > >>>------------------- > >>>*For cluster 18 Left Amygdala > >>>++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32- > bit]>>>+++ 37 voxels survive the mask > >>> > >>>*For cluster 54 Right Amygdala > >>>++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32- > bit]>>>+++ 200 voxels survive the mask > >>> > >>> > >>> > >>> > >>>_______________________________________________ > >>>Freesurfer mailing list > >>>Freesurfer(a)nmr.mgh.harvard.edu > >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >>> > >>> > >>> > >>-- > >>Douglas N. Greve, Ph.D. > >>MGH-NMR Center > >>greve(a)nmr.mgh.harvard.edu > >>Phone Number: 617-724-2358 > >>Fax: 617-726-7422 > >> > >>In order to help us help you, please follow the steps in: > >>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > >> > >>_______________________________________________ > >>Freesurfer mailing list > >>Freesurfer(a)nmr.mgh.harvard.edu > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >

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Vertex information lookup
by Pádraig Kitterick 28 Jul '08

28 Jul '08

Dear list, I wish to obtain information about a list of surface vertices, including their coordinates in MNI305 and Talairach spaces. Is there any tool that can provide this information at the command line? I can get the information by loading tksurfer and selecting the vertex, but this is slow for a long list of ROIs. I have found that the mris_info tool will give me the real coordinate of a surface vertex, but there is a discrepency between the information it provides and that obtained from tksurfer. For example, for a certain vertex, mris_info gives the coordinate (25.2, -93.5, 12.5). Loading the surface into tksurfer and selecting the same vertex gives a location of (24.90, -93.27, 12.26). The locations are obviously close, but the difference can't just be due to rounding errors. Padraig -- Pádraig Kitterick Graduate Student Department of Psychology University of York Heslington York YO10 5DD UK Tel: +44 (0) 1904 43 3170 Email: p.kitterick(a)psych.york.ac.uk

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First Level analysis
by Balaji Goparaju 28 Jul '08

28 Jul '08

Hi Doug and all, There is a problem when i try the individual statistics, I use the command selxavg3-sess -analysis LD-analysis -s LD-functional and i am getting an error: ERROR: cannot find volume matching /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg ERROR: loading nonpar reg /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold/006/mcextreg ------------------------------------------ ERROR: fast_selxavg3() failed\n The error seems to be something to do with a file needed to use motion correction regressors so i was wondering if the problem was because the software is not creating the file, or if there was any other way i could make freesurfer create the file. Thank you for any help!

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Preproc: Brainmasking
by Balaji Goparaju 28 Jul '08

28 Jul '08

Hi Doug and all, I used the new version of mkbrainmask-sess. It looks like the file is getting created but it cannot find fslmaths for avmaths. Is this error something to do with the freesurfer software itself, or is there anything I can do about it? Thu Jul 24 09:15:51 EDT 2008 /Users/balajigoparaju/Desktop/subjectdata mkbrainmask-sess -maskstem brain -fsd bold -s LD-functional -d /Users/balajigoparaju/Desktop/subjectdata -update ---------------------------------------- ------------------------------------------------ ------------------------------------------------ /Users/balajigoparaju/Desktop/subjectdata/LD-functional Thu Jul 24 09:15:52 EDT 2008 -------------------------------------------------- /Users/balajigoparaju/Desktop/subjectdata/LD-functional/bold mkbrainmask -i 006/f.bhdr -o masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0 -------------------------------------------------- ERROR: cannot find either fslmaths for avwmaths ERROR: mkbrainmask failed ERROR: mkbrainmask-sess failed Thank you for any help!

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AFNI /freesurfer aseg files problem
by Liat Levita 28 Jul '08

28 Jul '08

Hello, I wonder if anyone using AFNI converted freesurfer files has come across this problem (or can tell me if I making an error somewhere that I am just not seeing right now). I posted the same question on the AFNI board but haven't gotten feedback as yet. Here is the problem: After using freesurfer to get subcortical segmentations, I converted the resulting freesurfer files to AFNI format, which was fine - I had no problems doing that. However, when I try use these subcortical segmentation data files (subjectID_aseg_m_at3+tlrc) as masks to pull put PSC signal from each region of interest, I am getting an odd effect of right versus left; whereby left clusters output is fine ( voxel numbers are correct after 3dmaskave), but for the left it is very wrong. I have checked that the labels of the ROIs I am using are correct on AFNI GUI and they are. (code and output below) I am a bit at a loss; any help will be much appreciated. Liat AFNI Code used --------------- Foreach subj (xxx) foreach cluster (18 54) 3dmaskave -q -mask ${subj}_aseg_m_at3+tlrc -mrange ${cluster} ${cluster} \ "${subj}_all_runs_pscA_at3+tlrc" > ${subj}_fsROI_PSC_cluster_${cluster}.1D end end Output (get the same odd voxel output from all right hand side of the brain freesurfer generated ROIs) ------------------- *For cluster 18 Left Amygdala ++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit] +++ 37 voxels survive the mask *For cluster 54 Right Amygdala ++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit] +++ 200 voxels survive the mask

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Freesurfer July 2008