Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

very large csf spaces
by Krieger, Donald N. 16 Nov '15

16 Nov '15

This is a newbie question as this is the first grossly abnormal scan on which I need to run freesurfer. There are very large CSF spaces and only a rim of cortex and white matter for many regions. Freesurfer fails very early on. Before I post errors, I would like to try to get it to complete if there are pointers online. Is there a tutorial for running freesurfer on a grossly abnormal scan? Are there standard rules of thumb? Thanks - Don

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trac-all and mri_convert and FS license
by JuergenHaenggi 16 Nov '15

16 Nov '15

Dear FS experts we are running TRACULA on a Mac (OS X 10.7.5) and faced an error related to mri_convert. we then donloaded (as suggested in the FS archives) the modified file mri_convert.mac from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ and the initial error disappeared. However, when running trac-all FS claims that the license is not valid anymore, although there is no error when running recon-all. [Tschgiallos-iMac-2:~] tschgiallo% trac-all -prep -c /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/tracula_config_dudo.txt INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects INFO: Diffusion root is /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results/0028197/scripts/dmrirc.local -log /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results/0028197/scripts/trac-all.log -cmd /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results/0028197/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Mo 16 Nov 2015 09:57:39 CET mri_convert /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/prepare/0028197/0028197_dti.nii.gz /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results/0028197/dmri/dwi_orig.nii.gz mri_convert /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/prepare/0028197/0028197_dti.nii.gz /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/results/0028197/dmri/dwi_orig.nii.gz -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /Applications/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.222 2015/06/08 18:22:26 greve Exp $ reading from /Users/tschgiallo/Desktop/0_vivian_dudo/tracula/prepare/0028197/0028197_dti.nii.gz... Darwin Tschgiallos-iMac-2.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mo 16 Nov 2015 09:57:40 CET [Tschgiallos-iMac-2:~] tschgiallo% Any idea where the problem is? Thanks in advance Regards Jürgen ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. -----------------------------------------------------------------------------------------------------

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Help with desired (sub)cortical GM thickness
by Daniele Perrone 16 Nov '15

16 Nov '15

Hi Freesurfer Experts, I successfully used FreeSurfer to segment (sub)cortical GM using the "recon-all" pipeline, and I am wondering now how to control the final thickness of segmented GM. In other words, for a single subject, I want to obtain GM masks and parcels that are volumetrically thicker/thinner. Is there some FreeSurfer parameter I can vary? Thanks for your help, Daniele

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QDEC statistic problems correlation between lgi and experimental variable
by Bittner, Nora 16 Nov '15

16 Nov '15

Dear FreeSurfer experts, we calculated a GLM in qdec with our experimental variable (continuous), age and gender as covariates and LGI. We found significant clusters and corrected them for multiple comparisons with Monte Carlo Z Simulation. We found several significant clusters and looked at the correlation plots qdec displays automatically. In qdec we created labels from this clusters and mapped these to all subjects of our table.dat. Then we used mri_segstats to generate textfiles (.stats) listing our lgi values for each participant. Afterwards we correlated the lgi values with our experimental variable to plot the correlation. We used partial correlations and corrected for gender and age in SPSS. Sadly, we found no correlation between lgi values and our experimental variable anymore. How can this statistically be explained? Is there anything we did wrong? Thank you in advance! Best regards, Nora and Christian ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Unpacking errer after scanner upgrade
by Tan, Qingleng 16 Nov '15

16 Nov '15

Dear all, Our group is having trouble unpacking functional scans. If we ran the command: unpacksdcmdir -src ./all/ -targ ../bold/ -fsfast -run 5 bold nii f.nii We get the following error message: mri_convert ./all/64806020 ../bold/005/f.nii --sdcmlist ../bold//bold/005/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child process exited abnormally We have recently upgraded the scanner (from Trio to Prisma), and since we've never seen this error message before with Trio, it might be related to the scanner upgrade. We used both Freesurfer 5.1 and 4.5, but got the same error message. The flag with ‘-scanonly’ will run, and we could unpack anatomical scan without any issues. The log output looks like this (we’ve been trying to unpack runs 4-11): 99 PhoenixDocument err -1 -1 1 12 64766421 1 localizer ok 512 512 3 1 64818818 2 t1_mprage ok 256 256 160 1 64818847 3 ep2d3X3X3.5 ok 384 384 1 70 64816899 4 ep2dtask ok 384 384 1 76 64812417 5 ep2dtask ok 384 384 1 76 64806020 6 ep2dtask ok 384 384 1 76 64809896 7 ep2dtask ok 384 384 1 76 64803519 8 ep2dtask ok 384 384 1 76 64797142 9 ep2dtask ok 384 384 1 76 64790747 10 ep2dROI ok 384 384 1 101 64794623 11 ep2dROI ok 384 384 1 101 64789521 12 ep2d_resting ok 384 384 1 203 64784419 Please let us know if you have any ideas how to fix this issue. Thank you! -- Qingleng Tan, Graduate Student Department of Cognitive, Linguistic and Psychological Science Laboratory for Cognitive and Perceptual Learning Brown University Box 1821, 190 Thayer Street, Providence, RI 02912-1821

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Dimension mismatch between source and mask
by Isabelle Deschamps 16 Nov '15

16 Nov '15

Dear FreeSurfer experts, After running the following command: recon-all -autorecon2 -autorecon3 -subjid S08_FS I get the following error: /Volumes/FLYNN/ProjetPhonoBehavioralTMS/Freesurfer/S08_FS/mri \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n threshold mask volume at 5 ERROR: dimension mismatch between source and mask Darwin Isabelles-iMac.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 recon-all -s S08_FS exited with ERRORS at Mon Nov 9 18:56:20 EST 2015 I read in a post that it might be a problem with registration, so following a post found on the forum, I re-analyze this participant (from scratch) using: recon-all --autorecon1 -use-mritotal -subjid S08_FS then I ran recon-all -autorecon2 -autorecon3 -subjid S08_FS However, this did not solve the problem. Is there a workaround that I could use after the pial edits and running the -autorecon2 and 3? Thank you very much in advance, Isabelle

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Error in load_mgh
by Lars M. Rimol 14 Nov '15

14 Nov '15

Hi, I have downloaded freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and running MATLAB R2015b I get an error message when trying to use load_mgh. Any tips? >> [test, M, mr_parms, volsz] = load_mgh('<path>/<file name>.mgh'); ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in load_mgh (line 158) switch type (PS! I've tried chancing the file name to just lh.mgh but get the same error message. And the file(s) exist and the path is correct.) sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Bug in mrisComputeOriginalVertexDistances
by Andreas Schuh 14 Nov '15

14 Nov '15

Hi, I am just studying the FreeSurfer open source code (obtained from the read-only CVS, “dev” branch checkout instructions). It appears there is a slight mistake in mrisComputeOriginalVertexDistances. The following code computes the difference between v->y and vn->origy, where it probably should use v->origy as well. mrisurf.c:4093: xd = v->origx - vn->origx ; yd = v->y - vn->origy ; zd = v->origz - vn->origz ; Andreas

2 1

trouble with asegstats2table and aparcstats2table
by Elissa Ash 13 Nov '15

13 Nov '15

Dear Freesurfer support, I am very new to freesurfer and I thank you in advance for your assistance. I have been trying to run the group analysis tutorial (qdec) and I have encountered the following error messages. I was unable to generate the stats data tables in the tutorial and received the following types of error messages: 1) When trying to run asestats2table in qdec I get an error message that says that the subjects are not specified although they are. The $SUBJECTS_DIR is correct. I even encounter the same error when I just try to run asegstats2table --help (see below): tegmentum:group_analysis_tutorial gazzlab16$ asegstats2table --subjects 004 045 091 --meas volume --tablefile aseg_stats.txt File "/Applications/freesurfer/bin/asegstats2table", line 186 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax tegmentum:freesurfer gazzlab16$ asegstats2table --help File "/Applications/freesurfer/bin/asegstats2table", line 186 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax 2) When trying to run asestats2table I get an error message that says that at least one subject must be provided although they are. The $SUBJECTS_DIR is correct. I even encounter the same error when I just try to run aparcstats2table --help (see below): tegmentum:group_analysis_tutorial gazzlab16$ aparcstats2table --subjects 004 045 091 --hemi rh --meas thickness --tablefile aparc_stats.txt File "/Applications/freesurfer/bin/aparcstats2table", line 151 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print' tegmentum:group_analysis_tutorial gazzlab16$ aparcstats2table --help File "/Applications/freesurfer/bin/aparcstats2table", line 151 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print' I am not sure how to proceed. Thank you again for your assistance. Sincerely, Elissa -- Elissa Ash, MD, PhD Director, Center for Memory and Attention Disorders Department of Neurology Tel Aviv Sourasky Medical Center

2 2

recon-all error message
by Nicole Zurcher 13 Nov '15

13 Nov '15

Hi Bruce/hi all, Yes I am sure that I did not run out of disk space and I still get this error message for mris_calc. Do you have any suggestions? Thanks in advance Nicole > Message: 1 > Date: Mon, 9 Nov 2015 12:34:24 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] recon-all error message > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1511091234090.3068(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Nicole > > that's a very strange error. Are you sure that you didn't run out of disk > space? > > Bruce > On Mon, 9 Nov 2015, Nicole Zurcher wrote: > >> Dear all, >> >> One of my freesurfer recons is failing and I am not sure how to >> troubleshoot. >> >> This is the error message that I get at the end of the recon-all log >> file: >> >> mris_calc -o lh.area.mid lh.area add lh.area.pial >> WARNING: # of slices=-106 in header - assuming 124... >> read_signa([path]/surf/I.001): could not open file >> No such file or directory >> mris_calc: could not establish read access to 'lh.area'. >> No such file or directory >> >> and this is the command that appears in the recon-all.error >> CMD mris_calc -o lh.area.mid lh.area add lh.area.pial >> >> See attachment for entire recon-all log file. Any help is greatly >> appreciated. >> >> Thanks a lot >> Nicole >> >

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