Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.
by Douglas N Greve 03 Jun '13

03 Jun '13

Hi Rito, I don't think we report a total wm volume, do we? doug On 06/03/2013 12:56 PM, Ritobrato Datta wrote: > Hi Doug, > > Just following up on your reply sometime back - > Does total white volume include cerebellar wm vol also ? > > Please let me know. > > Thanks > > Rito > > ----- Original Message ----- > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > To: freesurfer(a)nmr.mgh.harvard.edu > Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT) > Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol. > > Total Gray includes the cerebellar gray > doug > On 05/24/2013 03:51 PM, Ritobrato Datta wrote: >> Hello All, >> >> Can someone address the following ? I sent this query yesterday but it fell through the cracks. >> >> I am using freesurfer 5.1 for my analysis. >> >> I am interested in calculating the whole brain vol (total Gray vol + total WM vol) excluding the CSF volume and cerebellum. >> >> Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol >> >> In all of the 79 subjects, when I compare the Total Brain Vol to SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain Vol I have calculated. >> >> Here are some measures - >> >> For 79 subjects - >> >> Average Total Brain Vol = 1038395.291 >> >> Average SupraTentorialVol = 979996.4684 >> >> Is that expected ? >> >> Is it possible that CSF vol is part of Total Brain Vol ? >> >> Any insight will be helpful. >> >> Thanks >> >> Rito >> >> _______________________________________________ >> 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. >> >> >> _______________________________________________ >> 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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combination of different surfaces across the group for mri_glmfit statistics
by Robert Schulz 03 Jun '13

03 Jun '13

Hi, I have two questions: 1. I have created specific surfaces in fsaverage rh for each of my 20 subjects. (xy.mgh) I'd like to run statistical analysis within the common surface area which is included in all subjects. Therefore I wonder how to combine those surfaces. My idea would be to add all surfaces and threshold the resulting surface by 20 ==> giving a final surface common to all of them. 2. How can I limit mri_glmfit to this final surface to run the statistical analysis only in this area, not in all of the hemisphere? Can anybody provide the appropriate commands for both issues? Thank you very much! Best wishes, Robert -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Astrid Lurati (Kommissarisch), Joachim Prölß, Matthias Waldmann (Kommissarisch) Bitte erwägen Sie, ob diese Mail ausgedruckt werden muss - der Umwelt zuliebe. Please consider whether this mail must be printed - please think of the environment.

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Bug report: fslregister within reg-feat2anat
by Chris Adamson 03 Jun '13

03 Jun '13

During the reg-feat2anat script fslregister produces errors. I tracked it to the argument parsing code 419 case "--fsvol": 420 if ( $#argv < 1) goto arg1err; 421 set fsvol = $argv[1]; shift; 422 set tmp = `fname2stem $fsvol`; 423 if(! $status) set fsvol = $tmp; 424 breaksw The reg-feat2anat script uses the following call: ./fslregister --s *** --reg ***+.feat/reg/freesurfer/anat2exf.register.dat --mov ***+.feat/example_func.nii --dof 6 --bins 256 --cost corratio --fslmat ***+.feat/reg/freesurfer/exf2anat.fsl.mat --fsvol brainmask --maxangle 90 --initfslmat ***+.feat/reg/freesurfer/exf2anat.init.fsl.mat --tmp ***+.feat/reg/freesurfer/tmp --out ***+.feat/reg/freesurfer/tmp/exf-in-anat.nii and the fsvol variable is eventually set ERROR: because line 422 fails. fsvol originally is just "brainmask" but it requires the full filename for fname2stem to work. Also, if I change the line 422 to $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz the rest of the script fails because it expects to just have "brainmask" not the full path. FS VOL FIRST brainmask Before stem brainmask /data/***********/mri/brainmask TMP ERROR: cannot determine stem FS VOL FIRST AFTER RETURN ERROR: -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental Imaging, Critical Care and Neurosciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road, Parkville,Victoria, 3052, Australia T 9906 6780 M XXXX XXX XXX E chris.adamson(a)mcri.edu.au www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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Defacing with mri_deface
by slehar＠nmr.mgh.harvard.edu 03 Jun '13

03 Jun '13

The script mri_deface which is called by recon-all with the -deface flag, requires the existence of two files /usr/local/freesurfer/stable5/average/face.gca /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca The former exists where it should, the latter does not exist at that location, although it can be downloaded from http://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads and gunzipped. When I copy it into a directory and call mri_deface directly, it works OK because it can find that image locally. But when I call recon-all with the -deface flag, it looks for the file where it does not exist, i.e. /usr/local/freesurfer/stable5/average/talairach_mixed_with_skull.gca Could someone with the appropriate permissions please copy that file to where recon-all expects to find it? Second question: If I call recon-all with the -deface flag, does it deface ALL the images in my SUBJECTS_DIR/$subjid/mri directory, or does it only deface a copy of orig.mgz to orig_defaced.mgz?

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use of anot_2_label
by LAOUCHEDI MAKHLOUF 03 Jun '13

03 Jun '13

Hi i used mri_annotation2label to extract the cortical labels. for this command we must specify which hemisphere (--hemi ?h) and i want to extract the brainstem which is not a lateralized structure, is there any command like mri_annotation2label to extract the brainstem ? thanks

2 1

Cortical thickness
by Joshua deSouza 03 Jun '13

03 Jun '13

Hello everyone, Please pardon my rather simple question I have done a GLM fit anlysis and have obtained a file sig.mgh alonf with a few others after the analysis.As I know, I do not have to create ROIs in order to do this. I also understand that doing a multiple comparison analysis just compares the regions of importance and evaluates them giving the most resilient cluster depending on the threshold. So, this does not give a thickness estimate. I would like to know how do I get the cortical thickness values from the results? If so, can I do it after glmfit? And thanks Doug for your help in the other questions that I had prior to this! Thank you

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(no subject)
by Shani Ben Amitay 03 Jun '13

03 Jun '13

Hello all I have created white matter surface of a non primate brain and I'm trying to use mris_make_surfaces to position the pial surface. The problem is that the resulted pial surface is miss-positioned-the 'growing' stops very close to the white surface (no gradient visible where it stops) Any idea what could be the reasons ? Thanks, Shani

2 1

bert recon-all errors, non-cuda
by Graham Wideman 03 Jun '13

03 Jun '13

2 1

mris_resample: Command not found.
by Barron, Daniel S 03 Jun '13

03 Jun '13

Hello, I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3. When I ran mri_cvs_check, my feedback was I needed to find "mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.ht… mri_cvs_register kicks off well, but eventually it ends with: "mris_resample: Command not found." I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly? I have attached a log file in case this helps. Cheers, Daniel

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autoreco3 error
by LAOUCHEDI MAKHLOUF 03 Jun '13

03 Jun '13

Hi i run recon-all -autorecon3 on a normal subject and after a while, it exited with errors, looking in the SUBJECTS_DIR/subj/scripts/error.log and recon-all.error and recon-all.log i found the following messages : error.log : mrisReadTriangleFile(../surf/rh.smoothwm): surface doesn't match ../surf/rh.inflated mrisReadTriangleFile failed. MRISreadOriginalProperties: could not read surface file smoothwm recon-all.error : . . . PWD /home_cluster/mlaouche/freesurf_makh/ctr5/scripts CMD mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere recon-all.log : mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... mrisReadTriangleFile(../surf/rh.smoothwm): surface doesn't match ../surf/rh.inflated No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ctr5 exited with ERRORS at Mon Jun 3 11:38:58 CEST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting thank you for your help

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Freesurfer June 2013