Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

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rendering problem
by Gabriel Gonzalez Escamilla 18 Jan '12

18 Jan '12

2 1

Re: [Freesurfer] selxavg3-sess issue in FSFAST
by Ivan Alvarez 18 Jan '12

18 Jan '12

Hello Doug, Ah! this was the root of the problem. A conflict was generated with the Stanford Vistasoft toolbox, which also contains a 'basename.m' file. Once removed from the Matlab path list, selxavg3-sess behaves normally. Thank you for the help! Kind Regards, Ivan Alvarez PhD Student Imaging and Biophysics Unit UCL Institute of Child Health 30 Guildford Street, London, WC1N 1EH On 17/01/12 17:48, Douglas N Greve wrote: > Hi Ivan, I can't pin down what the problem is. This is very strange. > There are a couple of things that you can try. First, start matlab and > run the command > which basename > This should return /home/ivan/freesurfer/fsfast/toolbox/basename.m > If it returns something else or multiple functions, then this is the > problem. > > doug > > > Ivan Alvarez wrote: >> Hello Doug, >> >> Please find attached the verbgen.sm5.lh/analysis.info file. >> >> Kind Regards, >> Ivan Alvarez >> >> PhD Student >> Imaging and Biophysics Unit >> UCL Institute of Child Health >> 30 Guildford Street, London, WC1N 1EH >> >> >> On 13/01/12 19:20, Douglas N Greve wrote: >>> Hi Ivan, can you send me verbgen.sm5.lh/analysis.info? >>> doug >>> >>> Ivan Alvarez wrote: >>>> Dear Freesurfers, >>>> >>>> I recently attempted my first FSFAST analysis following the >>>> tutorial on http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt >>>> <http://nmr.mgh.harvard.edu/%7Egreve/fsfast.intro.ppt> while using >>>> my own data. >>>> >>>> I stumbled across an error in selxavg3-sess which I can't decipher. >>>> The problem seems to arise when running the Matlab script >>>> fast_selxavg3.m andra returns: >>>> >>>> outtop = /media/data/analysis/FREESURFER_TEST/Project >>>> >>>> Extension format = nii.gz >>>> >>>> Error using basename >>>> >>>> Too many input arguments. >>>> >>>> >>>> Error in fast_ldanaflac (line 423) >>>> >>>> nuisregevname = basename(nuisreg,'dat'); % remove .dat >>>> >>>> >>>> Error in fast_selxavg3 (line 53) >>>> >>>> flac0 = fast_ldanaflac(analysis); >>>> >>>> >>>> >>>> I have looked through the Freesurfer documentation and mailing list >>>> but couldn't spot anyone with this issue. I am attaching the full >>>> log below, any insights would be greatly appreciated! >>>> >>>> >>>> >>>> >>>> ivan@sirsa:/media/data/analysis/FREESURFER_TEST/Project$ >>>> selxavg3-sess -sf sessid -analysis verbgen.sm5.lh >>>> >>>> Surface data fsaverage lh >>>> >>>> -------------------------------------------------------------- >>>> >>>> selxavg3-sess logfile is >>>> /media/data/analysis/FREESURFER_TEST/Project/log/selxavg3-sess-bold-verbgen.sm5.lh-120112125113.log >>>> >>>> >>>> -------------------------------------------------------------- >>>> >>>> preproc-sess -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -a verbgen.sm5.lh -nolog >>>> >>>> -------------------------------------------------------------- >>>> >>>> preproc-sess logfile is /dev/null >>>> >>>> -------------------------------------------------------------- >>>> >>>> $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ >>>> >>>> ivan >>>> >>>> setenv FREESURFER_HOME /home/ivan/freesurfer >>>> >>>> setenv SUBJECTS_DIR /home/ivan/freesurfer/subjects >>>> >>>> Linux sirsa 2.6.35-31-generic #63-Ubuntu SMP Mon Nov 28 19:29:10 >>>> UTC 2011 x86_64 GNU/Linux >>>> >>>> /media/data/analysis/FREESURFER_TEST/Project >>>> >>>> /home/ivan/freesurfer/fsfast/bin/preproc-sess >>>> >>>> -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -a >>>> verbgen.sm5.lh -nolog >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> instem f >>>> >>>> mc 1 f fmcpr >>>> >>>> stc 0 fmcpr >>>> >>>> sm 0 >>>> mask 1 brain >>>> >>>> Sess01 Template ----------------------------- >>>> >>>> mktemplate-sess -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -fsd bold -nolog -update >>>> >>>> >>>> >>>> Session: /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> ---------------- >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Detected input format at nii >>>> >>>> Sess01 Update not needed >>>> >>>> Run: 001 ---------------- >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Sess01 001 Update not needed >>>> >>>> Run: 002 ---------------- >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Sess01 002 Update not needed >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> mktemplate-sess completed >>>> >>>> Sess01 Mask ------------------------ >>>> >>>> mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -nolog -update >>>> >>>> ------------------------------------------------ >>>> >>>> /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Sess01 Update not needed for session-level mask >>>> >>>> Sess01 Update not needed for run 001 mask >>>> >>>> Sess01 Update not needed for run 001 meanval >>>> >>>> Sess01 Update not needed for run 002 mask >>>> >>>> Sess01 Update not needed for run 002 meanval >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> mkbrainmask-sess done >>>> >>>> Sess01 Registration ----------------------------- >>>> >>>> register-sess -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -fsd bold -dof 6 >>>> -per-run -nolog -update >>>> >>>> -------------------------------------------------------------- >>>> >>>> register-sess logfile is /dev/null >>>> >>>> -------------------------------------------------------------- >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> >>>> setenv SUBJECTS_DIR /home/ivan/freesurfer/subjects >>>> >>>> cd /media/data/analysis/FREESURFER_TEST/Project >>>> >>>> /home/ivan/freesurfer/fsfast/bin/register-sess -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -fsd bold -dof 6 >>>> -per-run -nolog -update >>>> >>>> >>>> freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >>>> >>>> Linux sirsa 2.6.35-31-generic #63-Ubuntu SMP Mon Nov 28 19:29:10 >>>> UTC 2011 x86_64 GNU/Linux >>>> >>>> >>>> >>>> Session: /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> ---------------- >>>> >>>> Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Run: 001 ---------------- >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> Update not needed >>>> >>>> Run: 002 ---------------- >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> Update not needed >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> register-sess completed >>>> >>>> Sess01 MC ----------------------------- >>>> >>>> mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -fsd bold -per-run >>>> -nolog -update >>>> >>>> Logfile is /dev/null >>>> >>>> ------------------------------------------- >>>> >>>> /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> >>>> RunList: 001 002 >>>> >>>> Sess01 001 Update not needed >>>> >>>> Sess01 002 Update not needed >>>> >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> mc-sess completed SUCCESSFULLY >>>> >>>> Sess01 To Surface ----------------------------- >>>> >>>> rawfunc2surf-sess -fwhm 5 -s Sess01 -d >>>> /media/data/analysis/FREESURFER_TEST/Project -fsd bold -hemi lh >>>> -nolog -update >>>> >>>> instem fmcpr >>>> >>>> outstem fmcpr.sm5.fsaverage.hemi >>>> >>>> ------------------------------ >>>> >>>> 1/1 Sess01 >>>> >>>> 1/1 Sess01 001 lh --------- >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> Sess01 001 Update not needed >>>> >>>> 1/1 Sess01 002 lh --------- >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> Sess01 002 Update not needed >>>> >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> rawfunc2surf-sess completed >>>> >>>> ---------------------------------------- >>>> >>>> Started at Thu Jan 12 12:51:13 GMT 2012 >>>> >>>> Ended at Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> preproc-sess done >>>> >>>> ------------------------------------------- >>>> >>>> /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> >>>> Thu Jan 12 12:51:14 GMT 2012 >>>> >>>> anadir = >>>> /media/data/analysis/FREESURFER_TEST/Project/Sess01/bold/verbgen.sm5.lh >>>> >>>> >>>> DoGLMFit = 1 >>>> >>>> DoContrasts = 1 >>>> >>>> UpdateNeeded = 1 >>>> >>>> ------------------------------------------ >>>> >>>> ------- matlab output -------------------- >>>> >>>> Warning: Unable to open display 'iconic'. You will not be able to >>>> display graphics on the screen. >>>> >>>> >>>> < M A T L A B (R) > >>>> >>>> Copyright 1984-2011 The MathWorks, Inc. >>>> >>>> R2011b (7.13.0.564) 64-bit (glnxa64) >>>> >>>> August 13, 2011 >>>> >>>> >>>> Warning: Duplicate directory name: /home/ivan/matlab. >>>> >>>> >>>> >>>> To get started, type one of these: helpwin, helpdesk, or demo. >>>> >>>> For product information, visit www.mathworks.com. >>>> >>>> >>>> >>>> >> >> >> >> >> >> >> >>>> /home/ivan/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>> >>>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>>> >>>> >>>> #@# Sess01 ############################### >>>> >>>> /media/data/analysis/FREESURFER_TEST/Project/Sess01 >>>> >>>> ------------------------- >>>> >>>> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ >>>> >>>> /home/ivan/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>> >>>> /home/ivan/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>>> >>>> /home/ivan/freesurfer/matlab/MRIread.m >>>> >>>> ------------------------- >>>> >>>> outtop = /media/data/analysis/FREESURFER_TEST/Project >>>> >>>> Extension format = nii.gz >>>> >>>> Error using basename >>>> >>>> Too many input arguments. >>>> >>>> >>>> Error in fast_ldanaflac (line 423) >>>> >>>> nuisregevname = basename(nuisreg,'dat'); % remove .dat >>>> >>>> >>>> Error in fast_selxavg3 (line 53) >>>> >>>> flac0 = fast_ldanaflac(analysis); >>>> >>>> >>>> >>>> >> ------------------------------------------ >>>> >>>> ERROR: fast_selxavg3() failed\n >>>> >>>> >>>> -- >>>> Kind Regards, >>>> Ivan Alvarez >>>> >>>> PhD Student >>>> Imaging and Biophysics Unit >>>> UCL Institute of Child Health >>>> 30 Guildford Street, London, WC1N 1EH >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >

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Re: [Freesurfer] control points
by Alana Shepherd 17 Jan '12

17 Jan '12

On the brainmask the intensity within the STG wm is either slightly lower than 110 or slightly higher, though at the exact location of the control points it is 110. Similarly on the wm.mgz the intensities range around 110. I am not sure what the intensity was at these points before the cp's were added and reprocessed. On 17/01/2012, at 1:36 PM, Bruce Fischl wrote: > Can you cc the list so others can answer? Is the wm in the brain.mgz in those regions darker than 110? Does putting control points there increase the intensity? It looks like a topological defect, but control points should help > > > > On Jan 16, 2012, at 9:34 PM, Alana Shepherd <alana.shepherd(a)unsw.edu.au> wrote: > >> Hi Bruce, >> Thanks for your fast reply. Sorry - I realise I may have been unclear in my explanation. The sections are not missing from the brainmask mgz file - as if they had been cut out during skull stripping - they are actually missing from the surfs and aseg definitions (see attached screen shot). >> Regarding skull stripping - I have been changing the skull strip parameters on an 'as-need' basis - so some of the subjects have a lowered ws thresh, others I have needed to use gcut to remove excess dura, and some have been fine with the default ws thresh. >> I hope this clarifies the issue, >> Cheers >> Alana >> >> <cp fail Screen shot 2012-01-17.png> >> >> >> >> On 17/01/2012, at 1:17 PM, Bruce Fischl wrote: >> >>> Hi Alana >>> >>> Have you tried changing the skull strip parameters? >>> >>> Cheers >>> Bruce >>> >>> >>> >>> On Jan 16, 2012, at 6:33 PM, Alana Shepherd <alana.shepherd(a)unsw.edu.au> wrote: >>> >>>> Hello, >>>> I am running version 5.0, and am finding in a few cases that some areas (most commonly STG) are missing from the original brainmask - after adding control points and re-running the pipeline, these regions are still not being picked up in the surfs or in the aseg. >>>> Can you suggest any other way of remedying this? >>>> Many thanks >>>> Alana Shepherd >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)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. >>> >>

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Pial extension into cerebellum
by Mahinda Yogarajah 17 Jan '12

17 Jan '12

Dear Freesurfer Experts, I have read the advice on the wiki regarding what to do when pial surfaces extend into the cerebellum. I had a few questions to clairfy things: 1) If I have made other (non-cerebellar) edits to the brainmask.mgz, and added control points can I simply do cp brainmask.mgz brain.finalsurfs.manedit.mgz edit the cerebellum voxels out on the brain.finalsurfs.manedit.mgz run recon-all -autorecon2-cp -autorecon3 -subjid name Will this then apply non-cerebellar and cerebellar edits (as well as control points) and give appropriate segmentations ? OR Do I have to make non-cerbellar edits to brainmask.mgz cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz make cerebellar edits to brain.finalsurfs.manedit.mgz run recon-all -autorecon2-cp -autorecon3 -subjid name Thanks. Mahinda

1 0

FSFAST v 5.1 group level volume analysis
by tapsya＠nmr.mgh.harvard.edu 17 Jan '12

17 Jan '12

Hi Doug, http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes states that "FSFAST - now masks the volume-based analysis to include only subcortical areas" and indeed, it looks like our group level volume results are in subcortical space only. We always use volume (native space full brain) analysis especially for sanity checks. At the group level, looking at analysis results in full volume (default brain mask) is essential for quality control and getting a feel of what is going on with the data. Is there a way to set up the volume analysis so that it is run for the whole brain (brain mask) at group level? Thank you! Best regards, Tapsya

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how to convert the *.annot to *.gii
by Zhang, Yuning 17 Jan '12

17 Jan '12

Hi, dear experts, In freesurfer , is there a way to convert the" *h.aparc.annot" file to Gifti file format so that caret can recognize it. thanks yuning

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bug in FS permutation
by Douglas N Greve 17 Jan '12

17 Jan '12

Hi Y'all, I have just found a bug in our implementation of the permutation test. It does not affect all permutations, so read on to figure out if it affects you. The bug is that the histogram that is created by the permutation simulation is always based on the last contrast in the analysis. The permutation p-value is computed from the histogram, so this means that the wrong histogram is being applied to the contrasts (except for the last contrast). This affects you IF: 1. You are doing permutation tests with mri_glmfit-sim or mri_glmfit to correct for multiple comparisons 2. You have more than one contrast 3. You are reporting p-values from a contrast that is not the last contrast on the mri_glmfit command-line 4. Note: the monte carlo simulations are not affected. Until I can find a better solution, the work-around is to run a separate instance of mri_glmfit for each contrast, then run mri_glmfit-sim separately for each mri_glmfit run. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Converting mgz to nii.gz
by Antonella Kis 17 Jan '12

17 Jan '12

Dear all, I am trying to convert my DTI image which was previous resampled to CVS space from an .mgz format to a .nii.gz format. When I resampled to CVS space I used the nearest interpolation. I used for converting this .mgz image to .nii.gz the mri_convert as you can see below: mri_convert --in_type mgz --out_type nii --out_orientation RAS /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz \ /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz I understood that --out orientation RAS states that I am flipping the image. Do I need to use this option? Even if I am using or not I see my image is having different direction than the .mgz image. Also while running with the option --out orientation RAS I saw that the program is doing a triliniar interp and I don't want to resample anymore my iamge just to converte this from mgz to nii. What is the best way I should do it? Thank you. Antonella

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Re: [Freesurfer] Converting mgz to nii.gz
by Lilla Zollei 17 Jan '12

17 Jan '12

Hi Antonella, If you are applying the morph to a mask file, then yes, the nearest neighbor interpolation shoudl be used. The masking option that you ask about below depends on whether you want to use wmparc to guide your masking (option 1) or whether you want to do the masking based upon intensity values found in the fa image (option 2). --Lilla On Tue, 17 Jan 2012, Antonella Kis wrote: > Dear Lilla, > > Many thanks for your reply and for your help. > > Regarding the way I resampled my fa data to the CVS space I was reading on the FSTutorial/Diffusion that if you wanted to resample a segmentation volume (such as wmparc or aseg) in CVS space, you would want to use the nearest neighbor (nearest) interpolation > option.The fa mask was calculated using the wmparc2diff as you can see below so I thought because I am using the wmparc which is a segmentation volume I should use for resampling the nearst interp. Please let me know if I am wrong. > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > Is this the right way to calculate my fa-masked or I should use all my fa data only: > > mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \ > $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz > Thank you very much! > Antonella > > ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Monday, January 16, 2012 5:39 PM > Subject: Re: [Freesurfer] Converting mgz to nii.gz > > > Hi Antonella, > > You should be able to just do > > mri_convert /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz > > BTW, when resampling your FA data to CVS space, I think you should be using trilinear interpolation. We only suggest the nearest neigbour option for segmentation and parcellation files. > > --Lilla > > On Mon, 16 Jan 2012, Antonella Kis wrote: > > > Dear all, > > > > I am trying to convert my DTI image which was previous resampled to CVS space from an .mgz format to a .nii.gz format. When I resampled to CVS space I used the nearest interpolation. > > > > I used for converting this .mgz image to .nii.gz the mri_convert as you can see below: > > > > mri_convert --in_type mgz --out_type nii --out_orientation RAS /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.mgz \ > > /media/2Tra/Antonella_2011/DTI_FS/dtrecon_cvs/C01_cvs/C01_dti/fa-masked.ANAT+CVS-to-avg35.nii.gz > > > > I understood that --out orientation RAS states that I am flipping the image. Do I need to use this option? Even if I am using or not I see my image is having different direction than the .mgz image. Also while running with the option --out orientation RAS I saw > that > > the program is doing a triliniar interp and I don't want to resample anymore my iamge just to converte this from mgz to nii. > > > > What is the best way I should do it? > > > > Thank you. > > Antonella > > > > > > > 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. > > > > >

1 0

Newbie question: mean/stddev for volumes and thicknesses in an atlas
by Inati, Souheil (NIH/NIMH) [E] 17 Jan '12

17 Jan '12

Hi All, I have a very small set of patients and I would like to compare the volumes of subcortical structures and thickness across the cortex to those of a large normative set. I don't need all the underlying data, just means and standard deviations. Is such a set of measures available? Thanks, Souheil

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Freesurfer January 2012