Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

command not found: tksurfer
by ZhangBo 02 Jun '20

02 Jun '20

External Email - Use Caution Hi teams, After installing freesurfer-7.0.0 in MacOS 10.15.4, I followed the testing guid in https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer. It is ok for freeview, however for tksurfer and tkmedit, I get errors "zsh: command not found: tksurfer", "zsh: command not found: tkmedit". Could you please give some advice about how to solve this? Thanks. Bo

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Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)
by Iglesias Gonzalez, Juan E. 01 Jun '20

01 Jun '20

Hi Elizabeth, segment_T1.sh uses a bunch of files in native space for initialization that you’d also have to deform, if you wanted to run it in MNI space. I think the easiest would be to run it in native space, and then warp the segmentation to MNI, using e.g., the registration given by CVS. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Elizabeth Haris <e.haris(a)unsw.edu.au> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, May 27, 2020 at 23:11 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152) External Email - Use Caution Hi guys, I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my subject, I have run recon-all, then run mri_cvs_register to obtain a brain image registered in MNI152 space. My questions are: 1. In recon-all, is there a way to specify registration to MNI152 space, or is it necessary to first run recon-all and then to run mri_cvs_register? 2. Is it possible to run the segmentHA script on the brain registered in MNI152 space? I’m unable to find where I would specify the use the cvs/norm.mgz (instead of the mri/norm.mgz file). And from what I can see in the script, the parameters set in lines 179/180/181 (below) point to fsaverage brain files, which don’t appear to be the correct targets for the new MNI152 brain; however, there are no corresponding output files in the cvs folder, so I am unsure how to define these parameters. 3. Is there anything I have missed and would also need to do to run the segmentHA script on an MNI152 brain? (I have previously run the script on the average brain and all went well.) 179 set ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz"; 180 set ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz"; 181 set LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt"; Thanks in advance, Elizabeth

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mri_vol2surf
by Nasr, Shahin,Ph.D. 01 Jun '20

01 Jun '20

Hi Surfers, Is there anyway to pass the full address of a surface to mri_vol2surf? To clarify, we are using surfaces that are saved outside <SBJ>/surf/ and we prefer not to relocate them every time that we want to use mri_vol2surf. Thanks

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Re: [Freesurfer] Convert mgz to nii
by Hua, Jessica 31 May '20

31 May '20

External Email - Use Caution Hi FreeSurfer experts, Also in case the code is different, how would I convert my T1.mgz file to a .nii file to be used in DTI analyses? Thanks! Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Convert mgz to nii
by Hua, Jessica 31 May '20

31 May '20

External Email - Use Caution Hi FreeSurfer experts, I would like to convert my .mgz parcellation file to a .nii file to be used in DTI analyses. How would I convert my participant's aparc+aseg.mgz file to a .nii file? Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

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Longitudinal study dimension mismatch
by KennethSPrice 30 May '20

30 May '20

External Email - Use Caution Hello Freesurfers! I am running a recon-all -long study and one of my subjects is giving me trouble. The brain segmentation volume for tp2 is greater than tp1. The scans were taken from the same machine with the same parameters, but the dimensions are mismatched: Volumes differ in dimension v1dim 512 512 32 1 v2dim 560 560 30 1 I am worried that dimension mismatch is causing an error in brain volume estimation. I have tried reslicing v1 to v2 dimensions but freesurfer did not like it. Would a dimension mismatch lead to significant volume differences, and is there any work around? \ Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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Cannot execute Binary file
by Graduate Imaging 30 May '20

30 May '20

External Email - Use Caution Hi, I recently downloaded fspalm, mri_surfcluster and mri_volcluster for freesurfer v6.0 from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/PALM/ and added them to the freesurfer/bin folder (had to replace the previous versions of mri_surcluster and mri_volcluster) and ran chmod a+x on all three to make them unix executable files. When I ran fspalm the permutation part of the command worked however when it reached the mri_surfcluster command it produced the following error in terminal "-bash:/Applications/freesurfer/bin/mri_surfcluster: cannot execute binary file" I'm running freesurfer on a MacOS system, are these the correct versions of the files I should be using? Thanks

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Re: [Freesurfer] Cannot execute Binary file {Disarmed}
by fsbuild 30 May '20

30 May '20

External Email - Use Caution Hello, The files mri_surcluster and mri_volcluster that you downloaded are patched versions for the linux distribution, so they won’t run on MacOS. But you should need to download them as they should already exist in the MacOS freesurfer distribution.  Or you should already have them under ./freesurfer/bin ($FREESURFER_HOME/bin in the freesurfer shell/environment) - under wherever your MacOS installation of freesurfer lives.   If you need to, you can download the freesurfer 6 MacOS distribution from https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads, install it on your own Mac and get those files. - R. On May 29, 2020, at 23:20, Graduate Imaging <graduate.imaging(a)gmail.com> wrote:Hi, I recently downloaded fspalm, mri_surfcluster and mri_volcluster for freesurfer v6.0 from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6..0.0-patch… added them to the freesurfer/bin folder (had to replace the previous versions of mri_surcluster and mri_volcluster) and ran chmod a+x on all three to make them unix executable files. When I ran fspalm the permutation part of the command worked however when it reached the mri_surfcluster command it produced the following error in terminal "-bash:/Applications/freesurfer/bin/mri_surfcluster: cannot execute binary file" I'm running freesurfer on a MacOS system, are these the correct versions of the files I should be using? Thanks

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AAL parcellation for Freesurfer
by Bastian Cheng 29 May '20

29 May '20

External Email - Use Caution Dear all, does anyone know if there is a surface parcellation file based on the AAL for freesurfer? I am aware that I could recon-all the MNI brain and project the atlas on the surface. (but maybe someone already did that) I spend some time googeling this, but haven't found it, therefore my question. all the best, Bastian <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virenfrei. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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mri_cnr label flag
by Pradyumna Bharadwaj 29 May '20

29 May '20

External Email - Use Caution Hi, I had a question about the -label flag in mri_cnr. 1) When you do not use the -label option and just use the following command: mri_cnr $FREESURFER_HOME/subjects/bert/surf $FREESURFER_HOME/subjects/bert/mri/norm.mgz The output is as follows white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white CNR = 1.983, gray/csf CNR = 0.907 lh CNR = 1.445 white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR = 1.952, gray/csf CNR = 0.943 rh CNR = 1.448 total CNR = 1.446 2) When you add -label $FREESURFER_HOME/subjects/bert/label/lh.cortex.label $FREESURFER_HOME/subjects/bert/label/rh.cortex.label to the first command, you get different (lower) cnr values. white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR = 1.389, gray/csf CNR = 0.644 lh CNR = 1.016 white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR = 1.353, gray/csf CNR = 0.652 rh CNR = 1.002 total CNR = 1.009 How is the lh.cortex and rh.cortex label changing the CNR computation? Any inputs or thoughts on this matter are greatly appreciated! Thanks, Prad

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Freesurfer May 2020