Freesurfer August 2013

freesurfer@nmr.mgh.harvard.edu

145 participants
268 discussions

Different results in surface and volume analyses
by Emily Boeke 07 Aug '13

07 Aug '13

Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in this region. These are the preprocess , mkanalysis, and selxavg commands I used for the surface vs. mni305: preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface fsaverage lhrh -mni305-2mm -fsd cond mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.mni305 -per-run -nskip 4 -stc down selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305 Why might we be seeing this activation on the surface map but not the volume one? Thanks! Emily

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error when using selxavg3-sess in retinotopy analysis
by Sepide Movaghati 07 Aug '13

07 Aug '13

Hi, I followed the steps for doing the retinotopy analysis. At the end I made my analysis as follows: mkanalysis-sess -a Retinotopy_ZY -surface self lh -TR 2 -retinotopy 36 -paradigm rtopy.par -fsd bold -fwhm 5 and then execute selxavg3-sess: selxavg3-sess –a Retinotopy_ZY –s session1 then I got this error which I do not how to solve it: outtop = /export01/data/sepid/subjects/ZY Extension format = nii.gz Error using fscanf Invalid file identifier. Use fopen to generate a valid file identifier. Error in flac_customize (line 47) flacnew.sourcesubject = fscanf(fp,'%s',1); Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I would appreciate if you help me through this. Regards, Sepide - I I - a

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Curvature, cortical thickness, LGI and artifacts
by Erin Browning 07 Aug '13

07 Aug '13

Hello-- Our dataset has 130ish scans with a bad temporal lobe artifact and a minor parietal lobe artifact. This artifact has affected the normalization and thus the white matter/gray matter selection, which we've manually fixed. However, the temporal lobe artifact is bad enough that chunks of data are missing in the surfaces. How will this affect curvature and LGI? We saw we can constrain our cortical thickness analyses to an ROI using mri_glmfit. Can we do this with curvature and LGI, and will having chunks of data missing affect readings elsewhere in the brain? Thank you, Erin Browning

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flip hemisphere of manual label
by Jonathan DuBois 07 Aug '13

07 Aug '13

Hi, Is there a way to transpose a manual surface label in fsaverage space onto the contralateral hemisphere? With tksurfer it opens in the opposite hemisphere but it does not correspond to the contralateral region. Thanks in advance. Best, Jonathan

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Re: [Freesurfer] Tracula question
by Anastasia Yendiki 07 Aug '13

07 Aug '13

Hi Alan - Try removing the "\" character from the end of the dcmlist definition. That's a change of line character. a.y On Wed, 7 Aug 2013, Alan Francis wrote: > Hi Anastasia: > > Here is the trac-all log. Please find attached the dmrirc file. > > csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep > -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 > > Too many ('s. > ERROR: must specify as many DWI dicoms as subjects > > Thank you so much. > > Alan > > > On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Yes, please attach the dmrirc and trac-all.log. Thanks! > > a.y > > On Wed, 7 Aug 2013, Alan Francis wrote: > > Hi Anastasia: > > For one brain I got this error message : > > csh::alanf@cerebro > [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all > -prep > -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 > > Too many ('s. > ERROR: must specify as many DWI dicoms as subjects > > I tried specifying the exact number of DWI dicoms but it is not working. Should I send you my > dmrirc for this brain? > > thanks, > > Alan > > > > > 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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set message
by Heather L. Urry 07 Aug '13

07 Aug '13

Hi folks, When issuing a recon-all command, I'm seeing the following message: set: Variable name must contain alphanumeric characters recon-all stalls and doesn't move forward (doesn't even create the subject directory). I'm using Freesurfer 5.3.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. In fact, we just upgraded to this version of Ubuntu from an older version of Mandriva and to this latest version of Freesurfer. recon-all did not produce this message before these two upgrades. Any help you can offer would be most appreciated! Thanks in advance. Best, Heather -- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155 email: heather.urry(a)tufts.edu phone: 617-627-3733 fax: 617-627-3181 http://ase.tufts.edu/psychology/ebbl

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5.3.0 patch
by Moran Cohn 07 Aug '13

07 Aug '13

Dear Freesurfer experts, I recently installed the stable 5.3.0 version of Freesurfer (CentOS 4, 64-bit) and encountered the known problem with the missing ribbon.mgz file when running -autorecon1 -autorecon2. I wonder how I can obtain the patch mentioned for this problem in the release notes, and would be very thankful for your help. Kind regards, Moran Cohn ________________________________ Dit e-mailbericht is alleen bestemd voor de geadresseerde(n). Het kan informatie bevatten die persoonlijk is en niet openbaar mag worden gemaakt krachtens wet- of regelgeving. Gebruik door anderen is niet toegestaan. Indien u niet de geadresseerde(n) bent, wordt u verzocht de verzender hiervan op de hoogte te stellen en het bericht te verwijderen

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mri_ca_train UCHAR/FLOAT
by Mark Plantz 07 Aug '13

07 Aug '13

Hello freesurfers, I am currently attempting to run mri_ca_train to create a .GCA atlas based of off a series of subjects. I am receiving the following error: *************************************************************************** processing subject CMH-3074, 1 of 10... mri_ca_train: segmentation file /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-3074/mri/seg_edited.mgz is not type UCHAR or FLOAT Is there an easy way to convert the file to UCHAR or FLOAT in FreeSurfer? Will this change the data/labels? Thank you! -MP

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Tracula question
by Alan Francis 07 Aug '13

07 Aug '13

Hi Anastasia: For one brain I got this error message : csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 Too many ('s. ERROR: must specify as many DWI dicoms as subjects I tried specifying the exact number of DWI dicoms but it is not working. Should I send you my dmrirc for this brain? thanks, Alan

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Re: [Freesurfer] trac-all inquiry
by Anastasia Yendiki 07 Aug '13

07 Aug '13

I see, you're using the old version of tracula (from freesurfer 5.1). In that version, you had to define the number of low-b images in the configuration file. I strongly recommend updating to freesurfer 5.3. A lot of things have improved in tracula since then. Also, in the future please attach any log files as separate attachments instead of pasting them into the body of your email - this causes the body of the email to exceed the limit allowable on the list. Thanks, a.y

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Freesurfer August 2013