Freesurfer August 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
152 discussions

quantifyHAsubregions.sh does not work
by Yang Molly 20 Aug '20

20 Aug '20

External Email - Use Caution Hi experts, When I tried to gathered the volumes of hippocampus subregions from all subjects by using the commend " quantifyHAsubregions.sh", the command did not work well. There's no error message in the terminal but no file was made after that command. My data was longitudinal data, so I did the longitudinal segment used “segmentHA_T1_long.sh”. Therefore, the exact command I run for results collection was "quantifyHAsubregions.sh hippoSF T1.long subhippallvolume.txt", I also tried to provide the subject directory explicitly as fourth argument like "quantifyHAsubregions.sh hippoSF T1.long subhippallvolume.txt /media/ubuntu/cxy/FreesT1/output.long”. The results was same, there was no file. All my subjects were pre-processed and segmentations using freesurfer version 7.1.0 on ubuntu 16.04. I attached screenshot of my terminal window and the script of quantifyHAsubregions.sh in my computer as below. Do you have any suggestions on how I could figure out this problem? Or other method to gather the results? Thanks a lot!! Molly

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FastSurfer with FreeSurfer version 7.1.0?
by Barbara Kreilkamp 20 Aug '20

20 Aug '20

External Email - Use Caution Dear all, I noticed FastSurfer also seems to run with a 7.1.0 FS version. Or is there any reason not to do this? Thank you, Kind wishes, Barbara

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Extracting LME results from label regions
by Mark Wagshul 20 Aug '20

20 Aug '20

External Email - Use Caution Dear Freesurfer experts, I have what seems like a simple problem, and I'm sure there is a method for doing this, hoping someone can give me some guidance. We have results from an LME model run on surface data, and then run through PALM to calculate FWE-corrected p-values from the LME. We now would like to extract the mean beta values from each anatomical label region, within regions that were significant at p-corrected < 0.05. The beta values (as well as the PALM p-values) are contained in an mgz surface file. So, what I think is needed is: 1) Create mask images for each individual label index, e.g. lh.caudalmiddlefrontal 2) Create mask image from PALM results, for p < 0.05 3) Multiply mask * label * beta, and calculate mean value in that region So, my simple question is what are the appropriate FS commands for performing this (or alternatively Matlab commands), or is there a simpler way or extracting these values? Thanks for any advice you can give us on this. Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.org<mailto:mark.wagshul@einsteinmed.org> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Creating Anatomical ROI with mri_volsynth
by Mauricio Watanabe Ribeiro 20 Aug '20

20 Aug '20

External Email - Use Caution Hello Freesurfer Experts, I'm trying to create a ROI based on the peak from a paper. The peak on MNI305 is X=22; Y=-71; Z=22 to use the mri_volsynth I transformed the CRS from MNI to rh.thickness with the formula: Vrh.thickness*inv(Trh.thickness)*R*T305*inv(V305) (as exemple 8 in https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) To obtain R I used: fslregister –s fsaverage –mov $SUBJECT_DIR/fsaverage/surf/rh.thickness –reg rh_thickness.dat So I created my spherical ROI with: mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/rh.thickness --pdf sphere --dim 1 1 1 1 --dim 1 1 1 1 --c_ras 54690 -13581 175 --o ROI.mgz However, when I try to use mris_fwhm --subject fsaverage --hemi rh --i ROI.mgz --o sphere.sm10.mgh I receive an error ERROR: MRISar1: Surf/Src dimension mismatch. Can someone help me with this?

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GPL license with exceptions
by Zhengjia Wang 20 Aug '20

20 Aug '20

External Email - Use Caution Hi, everyone, I'm developing a package that reads in files generated by FreeSurfer in some situations. The code was initially designed to publish in GPL-3. However, I noticed in your license agreement incompatible with this license. After reading some previous emails from this mailing list, I understand the reason why GPL license is discouraged. However, some of the dependencies of my package require a GPL-3 license and I couldn't get around with it. My question is: Can I publish my code under GPL-3 license but with exceptions that explicitly specify some data being processed are under FreeSurfer license? There have been several emails talking about this issue, but I still want to check and confirm the compatibility and/or possibility of GPL+exception. I'd appreciate it if you could provide some recommendations or requirements. The files that might be imported are: - $SUBJ/mri/*.mgz - $SUBJ/mri/transforms/* - $SUBJ/surf/* - $FREESURFER_HOM/FreeSurferColorLUT.txt Best. - Zhengjia Wang *PhD Student at Department of Statistics* *Rice University, Houston, TX, USA, 77005*

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Bug in quantifyThalamicNuclei.sh
by Iglesias Gonzalez, Juan E. 19 Aug '20

19 Aug '20

Dear all, Haewon Roh has discovered a small bug in quantifyThalamicNuclei.sh. We’ll fix it in the development version as soon as possible. In the meantime, we will post an amended version in the wiki; please see: https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei Thanks Haewon for picking up on this! /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

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quantifyHAsubregions.sh does not work
by Yang Molly 19 Aug '20

19 Aug '20

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Constraining analysis to ROI
by Erin Moe 19 Aug '20

19 Aug '20

External Email - Use Caution Hello Freesurfer experts, Is there a way to constrain an analysis to a label or ROI in QDEC? I have a group analysis looking at the effect of inflammatory markers on thickness however, I’d like to have the analysis be constrained within an ROI rather than whole brain to increase the power. I specified a label in mir_glmfit but the analysis seems to just mask out the rest of the brain rather than constraining to the ROI. Thank you for all your help! Erin

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Re: [Freesurfer] RBV PVC
by Nathalie Mertens 19 Aug '20

19 Aug '20

External Email - Use Caution Dear, I am not sure if the questions below were sent correctly to you, since I did not receive any copy of it. Please find my message below. Many thanks, looking forward to your reply. Kind regards, Nathalie Mertens Van: Nathalie Mertens <nathalie.mertens(a)kuleuven.be> Datum: dinsdag 18 augustus 2020 om 09:33 Aan: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Onderwerp: RBV PVC Dear, I do have some questions linked to RBV PVC implemented in Freesurfer: 1. Could you please tell me how the RBV PVC is acquired? Is the RBV PVC acquired based on Muller-Gartner (on a region-level, and based on only using gray- versus white matter), or when and how are the different regions from gtm_seg applied to obtain GTM? 2. What would be the advantage of using your technique compared to for instance sGTM? 3. Could you please tell me the difference in region-definition between aparc+aseg and the gtm_seg? (I saw that the latter contains less regions compared to aparc+aseg.) What is the reason to use the latter compared to the aparc+aseg, based on the definitions of the regions? (I know that gtm_seg is used which has a high resolution, but not quite sure, apart from the resolution, why you are not using aparc+aseg for the RBV PVC.) 4. Is there a mask applied to the gtm_seg to exclude regions that are located outside the brain? Many thanks for your answers. Kind regards, Nathalie

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" quantifyThalamicNuclei.sh" commend does not work..
by Haewon Roh 19 Aug '20

19 Aug '20

External Email - Use Caution Hi team. I'd like to collect all kinds of volumes of subjects' thalamic nuclei but the command " quantifyThalamicNuclei.sh" does not work in my mac book's terminal window. (there's no error message but any file was not made after that command ; please find attached screenshot showing the this problem) Before doing that command on terminal window, I made sure that every subject file had three files (ThalamicNuclei.v12.T1.FSvoxelSpace.mgz, ThalamicNuclei.v12.T1.mgz, ThalamicNuclei.v12.T1.volumes) after the process of segmenting thalamus. But, for hippocampal and amygdala subsegmentations, command of "quantifyHAsubregions.sh" is working well.. What is the difference between thalamic nuclei and hippoamygdala substructures for gathering all volumes into tabelfile ? my subjects were preprocessed with freesurfer version 6.0 and their substructure segmentations were made using freesurfer version 7.1. Does this make this problem? I attached screenshot of my terminal window as below.. Thank you always !! -- Hae Won ROH, M.D. H.P: +82-10-4341-8142 E-mail: rofree1st(a)gmail.com

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Freesurfer August 2020