Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

asegstats2table error with options --etiv and --no-vol-extras
by Rovai Antonin 19 Oct '20

19 Oct '20

External Email - Use Caution Hello, when using asegstats2table with the two flags --etiv and --no-vol- extras, I get the following error: ERROR: --etiv, cannot find EstimatedTotalIntraCranialVol in list It seems computing the ratio of volumes to etiv needs etiv to be included in the list (which by the way is not very useful because it is 100% by definition), but is there a way to get the ratios without including all the "extra" volumes? For instance using asegstats2table --tablefile "output.txt" --no-vol-extras --etiv --segno 225 I would expect to get the volume of CC_Anterior in % of etiv. Thanks for your help Antonin Hôpital Erasme - ULB Cliniques universitaires de Bruxelles Route de Lennik 808 - B - 1070 Bruxelles S www.erasme.ulb.ac.be Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

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Moving .nii atlas to surface space and create .annot file
by Maron M. 19 Oct '20

19 Oct '20

External Email - Use Caution Dear Freesurfer Team, I need to move an atlas file, Shen268 in 2mm (https://www.nitrc.org/frs/download.php/7977/shen_2mm_268_parcellation.nii.gz) from volumetric into surface space in order to do some analysis in MATLAB with it. Specifically, I need the atlas file as .annot and a .sphere (I think this would be from the anatomical template). So far, I have not succeeded. I believe it is some combination of recon-all, mri_vol2surf and mris_seg2annot, however the details are unclear. I think the initial problem is with the recon all. In this question (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63687.html) it says I should recon-all the "anatomical template". Could you elaborate which template that is? Its not the atlas file itself, but just some T1 in the same space? And that will give me the file necessary for the --reg command in mri_vol2surf, I guess? Sofar, I think this is what I have to do: 1) Recon-all -all -i "anatomical_template" (I am stuck here already, since I don't know what to recon-all here...) 2) mri_vol2surf --src atlas_file.nii --out outputfile_rh.mgz --hemi rh --projfrac 0.5 (--trgsubject fsaverage or —reg register.dat from recon-all?) 3) mris_seg2annot --seg outputfile_rh.mgz --s fsaverage --h rh --ctab-auto --o atlas_rh.annot I would be very thankful for any suggestions and support. Best and thanks a lot!

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display results with tksurfer
by Marina Fernández 19 Oct '20

19 Oct '20

External Email - Use Caution Dear Freesurfer experts, I would like to modify the values of the colorbar scale to display results in the inflated surface with tksurfer, in such a way that displayed values in the colorbar range from the minimum t- value detected to the maximum t value detected. I have tried to use the -fminmax flag, but the colorbar scale shows values from 0 to the maximum t value. Is it possible to limit values of the colorbar scale to min-max significant t values? On the other hand, is it possible to invert the colors of the colorbar scale (e.g., red for higher t values and yellow for lower t values)? Thank you in advance. Best regards, Marina

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mapping function of 3d coordinates of brain surface to latitude and longitude of a sphere
by 정태곤 19 Oct '20

19 Oct '20

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Display results
by Valentina Mancini 19 Oct '20

19 Oct '20

External Email - Use Caution Dear freesurfer experts, I'm trying to display the results of a study on a brain with Desikan and Killiany parcellation. Currently, I use tksurfer fsaverage, load the aparc.annot annotation, modify the colortable with values of interest and load it. However, in this way I can display only cortical regions. Any suggestions on how I could display cortical and subcortical regions at the same time? And where do I find an ordered list of cortical + subcortical structures to modify the values in each ROI? Thank you in advance for your help. Best, Valentina

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Error with pial delineation
by Julie Ottoy 19 Oct '20

19 Oct '20

External Email - Use Caution Dear Freesurfer team, I have a question regarding the freesurfer delineation of the subject in attachment. Here the pial delineation crosses the ventricle, instead of being delineating around the hippocampus. The light purple corresponds to the inferior lateral ventricle, and the dark purple corresponds to lateral ventricle segmentation. The hippocampus is the yellow segmentation. Would it be important to fix this for regional analyses? It seems as though the regions themselves were correctly assigned. What would be the appropriate way to fix this? Could control points be of any help? Thank you! Best regards Julie

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Re: [Freesurfer] recon-all -s <subject> -autorecon2-cp -autorecon3 error
by Douglas N. Greve 19 Oct '20

19 Oct '20

Those control points are still in gray matter. Please remember to post to the list, thanks On 10/9/2020 11:18 AM, Kazuki Sakakura wrote: > > External Email - Use Caution > > Thank you for continuously helping me. > > With your comment, I performed to put some control points in WM > (attached image). > However, the error was the same as before. > > Like I said before, I performed infant recon-all and there were some > slight defects in the medial temporal area (arrow). Therefore I tried > to modify the surface with control points. Is this a reason why > "autorecon2-cp -autorecon3" command had an error? If so, Do you know > any ways to modify the surface for infant recon-all subjects? >> >> Thank you. >> Best Regards >> >> Kazuki Sakakura > > ------------------------------------------------------------------------ > *From:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Sent:* Friday, October 9, 2020 8:47 AM > *To:* Kazuki Sakakura <hg3544(a)wayne.edu> > *Subject:* Re: [Freesurfer] recon-all -s <subject> -autorecon2-cp > -autorecon3 error > Those are all in gray matter. You need to make sure that they are all > in voxels that are clearly white matter > > On 10/8/2020 11:25 AM, Kazuki Sakakura wrote: >> >> External Email - Use Caution >> >> Thank you for replying. >> I'm sure I put control points in WM as the attached picture. >> >> I performed infant recon-all and there were some slight defects in >> the medial temporal area (arrow). Therefore I tried to modify the >> surface with control points. Is this a reason why "autorecon2-cp >> -autorecon3" command had an error? If so, Do you know any ways to >> modify the surface for infant recon-all subjects? >> >> Thank you. >> Best Regards >> >> Kazuki Sakakura >> ------------------------------------------------------------------------ >> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >> <freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas >> N. Greve <dgreve(a)mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> >> *Sent:* Wednesday, October 7, 2020 10:17 AM >> *To:* freesurfer(a)nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <freesurfer(a)nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject:* Re: [Freesurfer] recon-all -s <subject> -autorecon2-cp >> -autorecon3 error >> >> >> [EXTERNAL] >> >> I've never seen that one before. Can you post pictures of where you >> put the control points? Are you sure you put them in voxels that are >> clearly WM? >> >> On 10/6/2020 4:33 PM, Kazuki Sakakura wrote: >>> >>> External Email - Use Caution >>> >>> Hello FreeSurfer Developers, >>> >>> I'm attempting to compute recon-all after putting control point, but >>> for some of my subjects I get the attached error when I run the >>> recon-all -s <subject> -autorecon2-cp -autorecon3 command. >>> >>> >>> >>> I've searched the list and no similar errors have been reported. >>> Does anyone have any thoughts on how to trouble-shoot this one? >>> Also, Ive attached the recon-all.log in case it's of any use. >>> >>> 1) FreeSurfer version: >>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >>> >>> 2) Platform: Ubuuntu 14.04 >>> >>> 3) recon-all.log: see attached >>> >>> >>> Best Regards, >>> >>> Kazuki Sakakura >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto: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 Mass > General Brigham Compliance HelpLine at > http://www.massgeneralbrigham.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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Seed region in anatomical data for resting state fMRI data
by Gwang-Won Kim 19 Oct '20

19 Oct '20

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Help!
by Samar Fouda 16 Oct '20

16 Oct '20

External Email - Use Caution Hi! I am trying to run tracula- TRAC-All and I get this error message, i assumed it is because that bvals and bvecs needed to be predetermined but it seems like that is not the case and i am still getting the same error: Transform file should be eddy_correct/eddy log file or .mat file What do you think the problem is? Thanks so much for your help. -- *--* *Samar Fouda* *Post Doctoral Associate* *Emerge Research Program* *National Center for PTSD, Clinical Neuroscience Division* *Yale School of Medicine* *Samar.fouda(a)yale.edu <Samar.fouda(a)yale.edu>* *+1203285-7568*

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PETSC ERROR WHEN TRYING TO OPEN FREEVIEW
by Álvaro Deleglise 16 Oct '20

16 Oct '20

External Email - Use Caution Hi everybody, I've just installed FreeSurfer v6 in my ubuntu 20.04 SO, but I can't open freeview due to PETSC errors. I executed "freeview" in the console, and then the following messages appear: [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 8 FPE: Floating Point Exception,probably divide by zero [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named adeleglise by adeleglise Fri Oct 16 15:46:03 2020 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 I have seen other people with the same problem in the mail archive, but I didn't found any effective solution. Does anybody knows how can I solve it? Thanks in advance.

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Freesurfer October 2020