Freesurfer February 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
143 discussions

A couple of questions
by Zvi Baratz 16 Feb '20

16 Feb '20

External Email - Use Caution Hi all, Thank you for all your amazing work! I started using FreeSurfer recently and there are a couple of questions I was hoping someone here might be able to help me with: 1. Does anyone know of any way to silence recon-all's output or redirect it to stdout when called programmatically through nipype? I tried a couple of different approaches (using python's os.devull and creating a fake file-handle that does nothing on write() calls), but I can't seem to be able to get rid of it. Also, and I apologize if it exists and I simply missed it, I think it would be great to simply add a --quiet flag or something of the sort, considering the output is anyhow saved to a log file. 2. Is there any more documentation on recon-all's output other that the ReconAllOutputFiles <https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles> page? I've noticed a lot of info is missing there. I would be more than happy to contribute to it myself but I'm not sure what resources I can use to gather more information, and also I'm having trouble finding the corresponding documentation files on GitHub. Thanks again and all the best! Zvi

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About statistical analysis of volumetric results
by Halil Aziz VELİOĞLU 15 Feb '20

15 Feb '20

External Email - Use Caution Hi Mr/Mrs We treated a group of patients. We performed volumetric analysis in freesurfer before and after treatment. Is it correct to take volumetric values directly into a paired test? Or should we perform statistical analysis after dividing all values before and after treatment by "Estimated Total Intra Cranial Vol"? Is normalization by doing this way? Best regards Halil Aziz -- Öğr. Gör. Dr. Halil Aziz Velioğlu Kognitif Sinirbilim Anabilim Dalı

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ROI Analysis in a given label with Functional Constraint in FSFAST
by Star Xi 15 Feb '20

15 Feb '20

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Re: [Freesurfer] Cluster-wise correction for multiple comparisons
by Kim, Gwang-Won 14 Feb '20

14 Feb '20

Dear Douglas N. Greve, Thank you very much for your email. I ran mri_glmfit without --wis. Then I tried to ran mri_glmfit-sim as following: mri_glmfit-sim -glmdir g2v3.wls -2spaces -perm 1000 1.3 abs. But there is an error message “ERROR: design matrix is not orthogonal, cannot be use with permutation. If this something you really want to do, run with -perm-force”. How can I do if I want to solve this problems? Thanks, Gwang-Won ----------------------------------------------------------------------------------------------- Message: 6 Date: Fri, 14 Feb 2020 09:42:28 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Cluster-wise correction for multiple comparisons To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <fd8cd06d-6bcf-a108-4fbe-52080d93cf83(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" You don't need to specify a mask when you run mri-glmfigt-sim. When you ran mri_glmfit, you already specified the mask and that gets stored in the glmdir and then read by mri_glmfit-sim. Your mri_glmfit-sim command line look right (but you don't need the --bg 1 unless you really want to background the process, but using only one process will not speed it up). the other thing I want to point out is that (pseudo) weighted-least squares will not be taken into account by the permutation. I would rerun mri_glmfit without --wls and then run mri_glmfit-sim On 2/7/2020 3:01 PM, Kim, Gwang-Won wrote: > > Hi there, > > First, I ran "mri_glmfit" using mask including 4 ROIs(file name: > 4_ROI.label) as follows: mri_glmfit --glmdir g2v3.wls --y ces.nii.gz > --wis cesvar.nii.gz --fsgd 2group.fsgd --C group.diff.mtx --lable > 4_ROI.label? --surface fsaverage lh - --fwhm 5 ?eres-save. > > Second, I'm going to process "mri_glmfit-sim" to perform a > cluster-wise correction for multiple comparisons. > > Please let me know how to process "mri_glmfit-sim" using masks (file > name: 4_ROI.label) . > > Is it right? ?mri_glmfit-sim --glmdir g2v3.wls --perm 1000 3 abs > --2spaces --bg 1? > > Thank you, > > Gwang-Won >

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Pial surface not including parts of cortex
by Monica Bondy 14 Feb '20

14 Feb '20

External Email - Use Caution Dear Freesurfer experts, I was wondering if I could get some help with a problem that I keep experiencing. For some of the patients, their gray matter is not properly included in the pial surface. I have tried tkmregister and using control points but neither have been successful. I have read on a separate thread that editing the wm.mgz may be helpful but could I have some guidance on this please? Also, I know it can be difficult to tell the problem based on the description so please let me know if I can send something over to help. I'm still very much learning how to work freesurfer so I really appreciate your help. (Note: I am using version 5.3) Thank you, Monica

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make average subject/ highres fMRI data
by Nasiriavanaki, Zahra 14 Feb '20

14 Feb '20

Dear Freesurfer experts Hi I got an error when I was trying to make an average subject. I attached the log file. I appreciate if you could please let me know what the problem is. make_average_subject --out avgsubject --subjects subj1 subj2 subj 3 labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from Linux bee.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s avgsubject exited with ERRORS at Mon Feb 10 10:43:37 EST 2020 For more details, see the log file /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Request for access to the freesurfer mailing list
by Varun Chandran 14 Feb '20

14 Feb '20

External Email - Use Caution Dear Freesurfer committee, I would like to use the freesurfer mailing list to post my doubts about the cortical thickness analysis pipeline. Therefore, could you please provide me the access to post my doubts on the same? thanks, kind regards, Varun Arunachalam Chandran PhD in Neurosciences, School of Psychology and Language Sciences, University of Reading, Berkshire, UK

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watershed, saving issue
by Kirill Elin 14 Feb '20

14 Feb '20

External Email - Use Caution Hallo everybody, I am not entirely sure whether this is FreeSurfer error actually. I am doing first recon all which completes without errors. Then I need to create BEM surfaces using the FreeSurfer watershed algorithm for MEG data analysis using MNE-Python. So the next command in the terminal is: mne watershed_bem --subject subjectname And it runs e.g. till: mri_watershed ru_nivcsw 12490 mri_watershed done and quits with errors like: File "/work/modules/Ubuntu/14.04/amd64/common/anaconda3/latest/envs/neuroimaging/lib/python3.6/site-packages/mne/utils/check.py", line 143, in _check_fname raise IOError('Destination file exists. Please use option ' OSError: Destination file exists. Please use option "overwrite=True" to force overwriting. Now, it is unclear what file destination file is meant. This happens on several machines for all participants. --overwrite option does not help. The correct outcome should include bem folder with resulting files and also watershed subfolder with resulting files. Here and the files in bem folder are missing and there are files only in watershed subfolder. FreeSurfer 6.0.0., Ubuntu Thank you in advance. Sincerely yours, Kirill

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Systematically Navigating .sphere vertices
by Mcnorgan, Christopher 14 Feb '20

14 Feb '20

External Email - Use Caution I’m interested in working with data mapped to the .sphere icosohedrons. I understand from a response from Doug back in 2017 that: waveforms = fast_vol2mat(MRIread('waveform.nii.gz')); will give me a v x time matrix of values from my functional values. In the case of fsaverage, I believe I can expect somewhere around 160K rows, 1 per vertex, for each hemisphere. I was wondering how I might be able to determine the neighbors (i.e., vertices connected by an edge) for any vertex v? Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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study design flair T1
by Renew Andrade 14 Feb '20

14 Feb '20

External Email - Use Caution Dear FreeSurfer experts: I am dealing with a crossectional retrospective case control study where I don't have all subjects with the same inaging protocols. I do have T1 for all of them although some have T2 others FLAIR others T2+FLAIR (besides T1 for all of them). My question is regarding VBM can I do inference on images with different characteristics? Or should them all have T1 + T2 or T1 + FLAIR. I guess this is the case that is all subjects should be processed with the same protocols. This is in Multiple Sclerosis by the way just in case it matters. Sincerely, Andrade. Sent from my iPhone

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Freesurfer February 2020