Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

19 Sep '14

Hi all I was wondering whether it’s possible to get the talairach coordinates associated with each label in the segmentation. I would like to use Freesurfer’s segmentation for analysis in Matlab.How to create a text file with the talairach coordinates of each label (or of a specific label, by label number), Thanks

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Question about Voxel Quantification with Thresholds
by Karishma Smart 19 Sep '14

19 Sep '14

Dear all, Is there a way to get a count of the voxels in a manually drawn ROI while retaining each voxel's intensity value? *In particular, I would like to get a count of how many voxels in this manually drawn ROI fall above and below an assigned intensity threshold.* I have used mri_segstats to quantify the number of voxels in a particular ROI that I have drawn manually (i.e. not using aseg). However, in doing so (I created a label for the ROI and used mri_segstats to count the number of voxels in the label), I assigned each voxel the intensity of the label, thus losing the intensity information. Any guidance or assistance would be greatly appreciated. Preferably, it would be helpful if anybody knows a way to do this that is not modality-dependent. Thank you in advance for your help, Karishma -- Karishma Smart B.A. Biological Sciences Cornell University Class of 2013 Boston University School of Graduate Medical Sciences Class of 2015

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Converting GIFTI files to Freesurfer files
by Reza Rajimehr 19 Sep '14

19 Sep '14

Hi, To convert GIFTI files to the Freesurfer files, I just need to do something like this? mris_convert F99.R.inflated.74k_f99.surf.gii rh.inflated Thanks, Reza

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ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
by Mahmoud 19 Sep '14

19 Sep '14

Dear all, After running "recon-all -i $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm -subject case018_tp2 -all" I'm always getting the following error and really don't know how to fix. Could anybody please help me. The recon-all.log file is attached. Thank you, Mahmoud Reporting on 70 segmentations mri_segstats done /usr/local/freesurfer/subjects/case018_tp2/label #-------------------------------------------- #@# BA Labels lh Thu Sep 18 20:23:27 EDT 2014 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /usr/local/freesurfer/subjects; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject case018_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = case018_tp2 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s case018_tp2 exited with ERRORS at Thu Sep 18 20:23:27 EDT 2014 For more details, see the log file /usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log

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HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion
by Matthieu Vanhoutte 19 Sep '14

19 Sep '14

Dear Freesurfer's experts, I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data. The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006). I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage ( https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping) with no download link... Where can I find this package and how to use it ? Many thanks ! Best, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France

2 4

segmentation fault mri_convert Ubuntu 14.04
by Alessandra Griffa 19 Sep '14

19 Sep '14

Dear all, I am running FreeSurfer version [recon-all,v 1.313.2.6 2010/08/04] on an Ubuntu machine. After updating my system from Ubuntu 12.04 to Ubuntu 14.04 I get a segmentation fault when I try to resample images using mri_convert: /mri_convert -vs 1 1 1 /folder/original_image.nii.gz /folder/resampled image.nii.gz // //$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $// //reading from /folder/original_image.nii.gz...// //Segmentation fault (core dumped)/ Any help on this? (for consistency with an on-going study I would like not to install a newer FreeSurfer version) Thank you very much! Alessandra -- ------------------------------ Alessandra Griffa Doctoral assistant Signal Processing Laboratory 5 EPFL STI IEL LTS5 ELD 233 (Bâtiment ELD) Station 11 CH-1015 Lausanne Tel.: +41216934807 web: http://lts5www.epfl.ch/ personal page: http://people.epfl.ch/alessandra.griffa?lang=en ------------------------------

2 1

Freeview screenshot automation questions
by Eric Xiuming ZHANG 19 Sep '14

19 Sep '14

Dear FreeSurfer experts, I understand that > freeview -v brain.nii.gz -ss screenshot takes the screenshots and quits the freeview. Regarding this, I have the following two questions. (1) Is it possible to suppress the redundant GUI flashing? It is really a pain when many images are batch-processed, because the GUI keeps flashing up and closing. (2) Is it possible to take multiple screenshots with one session? I wish to screenshot multiple slices of one image. I have tried > freeview -v brain.nii.gz\ > -viewport sagittal -slice 80 127 127 -ss sag1 \ > -viewport sagittal -slice 127 127 127 -ss sag2 \ > -viewport sagittal -slice 156 127 127 -ss sag3 \ However, the session ends right after the first -ss, producing only one screenshot (sag1.png). I can surely do freeview -v brain.nii.gz 3 times to get these 3 screenshots, but that is very inefficient. Thank you very much for your help in advance! Best regards, Xiuming ZHANG (Eric) Xiuming ZHANG (Mr.) :: Department of Electrical & Computer Engineering (ECE) :: National University of Singapore (NUS)

2 1

fsaverage subject does not exist in SUBJECTS_DIR
by Mahmoud 18 Sep '14

18 Sep '14

Dear All, I ran the following script: #!/bin/bash SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm -subject case022_tp2 -all and got the error below at the end. Could anybody please let me know how to fix it. Thank you, Mahmoud Reporting on 70 segmentations mri_segstats done /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label #-------------------------------------------- #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014 INFO: *fsaverage subject does not exist in SUBJECTS_DIR* INFO: Creating symlink to fsaverage subject... cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - ln: *failed to create symbolic link './fsaverage': Operation not supported* mri_label2label --srcsubject fsaverage --srclabel /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = case022_tp2 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/hgfs/DBSI/volumetric/MGZ FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 PDT 2014 For more details, see the log file /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] displaying a single label from aparc in tksurfer
by Daniel Carey 18 Sep '14

18 Sep '14

Hi Maria, You can display a single label (or labels) in tksurfer by loading the aparc annotation onto fsaverage; then, simply click on the label you're interested in, and click File, then Label, and Save Selected Label. This will let you save out a single label from aparc, which can these easily be loaded onto fsaverage on its own. You can of course also overlay multiple labels in tksurfer that you've saved out in this way (and naturally change colour schemes if you're so inclined). Best, Dan --- On 18 Sep 2014, at 22:03, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > displaying a single label from aparc in tksurfer Daniel Carey Marie Curie Ph.D. Fellow, Centre for Brain and Cognitive Development, 32 Torrington Sq., London WC1E 7HX email: d.carey(a)bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey

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quick quality assessment for MPRAGE images
by Wegbreit, Ezra 18 Sep '14

18 Sep '14

Dear Freesurfer Users, I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values. However, some of the MPRAGE scans are contaminated by subject motion, but the extent of this varies from scan to scan. Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all? Thanks! Ezra *___________________________________________________________* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Medical School (401) 432-1615 ezra_wegbreit(a)brown.edu (preferred) ewegbreit(a)lifespan.org *___________________________________________________________*

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