Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

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

2 1

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 >> >

3 2

Re: [Freesurfer] qdec analysis with ICV
by Hirsch, Gabriella 13 Nov '15

13 Nov '15

Thanks for the suggestion David. I tried it but I still got the same error :/ Gabriella From: David Vazquez [mailto:dvazq002@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV Hi Gabriella. I'm not an expert, but I've had this problem too. Reduce the number of digits for ICV by converting it be cm^3 instead of mm^3. Also get rid of some decimal places. It works for us. Good luck. -David On Fri, Nov 13, 2015, 8:10 AM Hirsch, Gabriella <Gabriella_Hirsch(a)meei.harvard.edu<mailto:Gabriella_Hirsch@meei.harvard.edu>> wrote: Hi Freesurfer Experts, I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format). However, I am getting this error: Normalized matrix condition is 1e+08 Design matrix ------------------ 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it? Thank you! Gabriella • Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not “Reply All.” After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly. _______________________________________________ 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 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. • Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not “Reply All.” After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.

2 4

Trackvis/ Diffusion Toolkit
by Alan Francis 13 Nov '15

13 Nov '15

Hi Anastasia: It was great to meet you at the connectivity course at Martinos. I have been using Trackvis to examine the white matter tracks between the anterior insula and the Dorsal ACC. In line with your instruction, I created ROIS at each of these regions. However, the WM tracks generated do not appear to connect. I have attached a screenshot. What is the command that one would use to connect the ROIs? thanks so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

2 3

counting voxels in seeds
by André Schmidt 13 Nov '15

13 Nov '15

Dear FS experts, Using recon-all I defined 82 regions for a probabilistic tractography analysis. To address volume differences across regions, I like to normalize the obtained streamlines by the number of voxels in each regions. Is there an easy way to count voxels within each of my 82 regions? Thanks for your help André

2 1

qdec analysis with ICV
by Hirsch, Gabriella 13 Nov '15

13 Nov '15

Hi Freesurfer Experts, I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format). However, I am getting this error: Normalized matrix condition is 1e+08 Design matrix ------------------ 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it? Thank you! Gabriella * Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.

1 0

Orientation of neural dipoles from Freesurfer
by Daniel Lindh 13 Nov '15

13 Nov '15

Hi, I am looking for a way of figuring out the orientation vector of the neurons within a voxel. That is, in which direction is the dipole of the neurons pointing at. This could be possible to calculate if there is a way of determining the position of the inner and outer layer for each voxel, which I am assuming is something Freesurfer does when it calculates gray matter thickness. If you could direct me to some relevant literature or an online tutorial I would be extremely grateful. best regards Daniel

2 2

Longitudinally processed thickness measures
by Worker, Amanda 13 Nov '15

13 Nov '15

Hi All, I have processed some longitudinal data (0, 1 week, 4 weeks) using the advised longitudinal stream. This is a healthy control sample and I wasn't expecting to see any differences in cortical thickness over the time points. Looking at some of the measures I have noticed that something doesn't seem quite right e.g. for one subject the insula measures: Cross-sectional Longitudinal Base A 2.835 3.016 B 2.721 1.864 C 3.050 3.107 3.098 The majority the longitudinally processed data looks reasonable, but there are a few instances where one timepoint looks completely different. Do you have any ideas if something may have gone wrong? I have attached the recon-all.log files for the template and the 3 longitudinally processed timepoints. Thanks in advance for your help, Amanda

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer