Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Change in volume driven by SA or CT?
by Meike Hettwer 04 Aug '20

04 Aug '20

External Email - Use Caution Dear Freesurfer Experts I am trying to get more information about a cluster indicating a change in cortical volume as a function of a continuous variable. I am currently considering different approaches to find out if this change in volume is primarily explained by a change in surface area or cortical thickness. Is there a standard procedure that freesurfer users go for to do this? (Otherwise I would probably extract volume, SA and CT values from the cluster and run an external analysis.) Thanks a lot, Doro

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Recon-all error when refining pial surfaces with T2 FLAIR
by Pankush Kumar 04 Aug '20

04 Aug '20

External Email - Use Caution Hello, I am a student using freesurfer 7.1.0 having some trouble with recon-all on some subjects. I am trying to calculate pial surfaces by adding FLAIR images to my T1 (already processed on recon-all beforehand), but encounter the following error: Starting loop over 121584 vertices vno = 0, t = 1.21632 vno = 20000, t = 3.38757 vno = 40000, t = 8.77043 vno = 60000, t = 11.8685 vno = 80000, t = 14.6273 error: Numerical result out of range error: MRIhistogramLabelRegion: constant image Log is attached. Other subjects get stuck on the vno = 80000 step and run for days without progress. No artifacts in any of the images, but some have obvious structural variation such as enlarged and misshapen ventricles. Thank you, any help would be greatly appreciated! Sincerely, Pankush Kumar

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Local GI vs. Folding Index
by Alexopoulos, Dimitrios 03 Aug '20

03 Aug '20

External Email - Use Caution The aparc.stats file contains a Folding Index measure for each cortical parcellation. How is this measure determined and how is it different from the one calculated using the -localGI flag after precessing a subject? Jim Get Outlook for Android<https://aka.ms/ghei36> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Converting sulc files
by Alexopoulos, Dimitrios 03 Aug '20

03 Aug '20

External Email - Use Caution Is there a command that will convert the ?h.sulc to ascii, i.e. depth at each vertex? Get Outlook for Android<https://aka.ms/ghei36> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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mrisurf note for bevin?
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 03 Aug '20

03 Aug '20

Hi all, I am using a freesurfer 6 dev version of tkmedit and opening one of my brain scans that was processed through 7.1 (I copy the ?h.pial.T1 -> ?h.pial to accept the -surfs command). I get the note mrisurf.c:4077 trial: 0 nextPendingSIze:2 BEVIN IS LOOKING FOR AN EXAMPLE THAT DOES THIS after one of the pial loads. Is this a subject that the FS devs would like for debugging? Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Labels from thalamic parcellation
by Jason Smucny 03 Aug '20

03 Aug '20

External Email - Use Caution Hello Freesurfer Team, I am running thalamic parcellation using freesurfer 7.1 and the program (http://freesurfer.net/fswiki/ThalamicNuclei) is outputting thalamic labels e.g. 8108, 8109, 8208 etc. I was wondering if you might point me towards a dictionary so I know which thalamic subregion corresponds to each numbered label. Thank you, Jason

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ctx-lh-corpuscallosum
by Ian 03 Aug '20

03 Aug '20

External Email - Use Caution Hi Freesurfers. There is a "ctx-lh/rh-corpuscallosum" label in Freesurfer, but the Corpus Callosum is not considered to be in the cortex. Can you explain precisely what this label refers to? Thanks, Ian

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Dimension mismatch
by Meike Hettwer 03 Aug '20

03 Aug '20

External Email - Use Caution Dear freesurfer experts I got an error that I don't understand when running mri_glmfit on cortical volume in the right hemisphere. I only have one group and one covariate of interest (+ age and ICV). ERROR: dimension mismatch between y and X. y has 102 inputs, X has 105 rows. I attached the log, fsgd and mtx files. I included 105 subjects and I don't get any errors when running the same command for surface area or cortical thickness. I can run my analysis for cortical volume in the left hemisphere, but not in the right hemisphere. The error message sounds like there is data missing for 3 subjects, but as far as I can see, that is not the case. Thanks a lot for you help, Meike

2 1

mri_aparc2aseg: how to remove redundant output labels?
by Ellen Ji 03 Aug '20

03 Aug '20

External Email - Use Caution Dear experts, I am running mri_aparc2aseg using two annotations as input (one for each hemisphere), each with 159 labels, and wish to end up with a single output segmentation of 318 labels. However, when I run the below, this is not the case: mri_aparc2aseg \ --s subject1 \ --annot 500_sym.aparc \ --wmparc-dmax 2 \ --labelwm \ --hypo-as-wm \ --o subject1/mri/parcellation.nii.gz In fact, the output has 680 labels rather than 318 labels. A few questions. - How can I see what exactly the 680 label names are (how to extract from the .nii.gz output file)? Currently, I have just quantified it to be 680 by doing this in matlab: gunzip('parcellation.nii.gz') a = MRIread('parcellation.nii'); u = unique(a.vol(:)); length(u) % total number of labels - I believe the extra labels are from the Freesurfer LUT. How can I make sure they are not added when running mri_aparc2aseg? (such that only my annotation labels are included in the output) Thank you very much, Ellen ***** Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji(a)bli.uzh.ch homanlab.github.io/ellen/

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Gray matter volume image per group
by Oana Georgiana Rus 03 Aug '20

03 Aug '20

External Email - Use Caution Dear Freesurfer Community, I want to have an image of the average gray matter Volume in each of my 3 groups, and I did not find a good way to do it. I easily obtained an image from the GM thickness and area by using make_average_subject in each of my 3 groups (young musicians, old musicians and old nonmusicians). Thereby in the surf subfolder I could find an image of these 2 measures. Could anybody give some helpful hint. I am using FreeSurfer 6.0 on an Ubuntu Machine.18.04.4 LTS. Best regards, Georgiana

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