Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30078 discussions

ERROR: Talairach failed
by Bouchra Guelib 27 Jul '22

27 Jul '22

External Email - Use Caution I have a nifty MRI, converted to mni 305 space when I apply recon-all, I have this error: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0525, pval=0.0034 < threshold=0.0050) Command exited with non-zero status 1 @#@FSTIME 2022:07:22:11:11:46 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M 6628 F 0 R 266 W 0 c 0 w 1 I 0 O 0 L 2.89 2.56 1.45 @#@FSLOADPOST 2022:07:22:11:11:46 talairach_afd N 4 2.89 2.56 1.45 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. see http://secure-web.cisco.com/11upxJF_-cI-E4FBY17KCMERFQk_Wf_2bOtw3CCmUNLSGGV… ERROR: Talairach failed! what should I do? -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: Guelibbouchra(a)gmail.com

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TRACULA -bedp parallel processing
by Salar Dini, Elaheh 27 Jul '22

27 Jul '22

External Email - Use Caution Hello, I have tried to create a text file with command lines that can be run in parallel by using trac-all -bedp -c <config file> -jobs Parallel. When I use this command three text files are produced named: pre.Parallel, post.Parallel, and Parallel. Should I just use Parallel as a source for command lines? What are pre.Parallel and post.Parallel for? I am attaching my Configuration file, pre.Parallel, post.Parallel, and Parallel to this message as well. OS: Centos 7, Freesurfer version: 7.2.0 Thank you for your help. Kindly, Ela

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Understanding ?h.sphere.reg
by Salar Dini, Elaheh 27 Jul '22

27 Jul '22

External Email - Use Caution Dear freesurfer experts, I was wondering if ?h.sphere.reg files have any coordinates in space tagged to them? What I actually mean is I'm using TRACULA which itself use the following files from mri and surf folder (all created by running recon-all on T1 image): aparc+aseg.mgz, brain.mgz, brainmask.mgz, orig.mg, T1.mgz and ThalamicNuclei.v12.Ta.FSvoxelSpace.mgzlh.thickness,rh.thickness,lh.white,rh.white,lh.sphere.reg,rh.shere.reg. I have all these files (except ?h.thickness and ?h.sphere.reg) in new coordinates in space created by co-registration. The pipeline we use to create recon-all results is almost the same as freesurfer pipeline with a slight difference in autorecon1 step, so the final results are almost always the same but the coordinate of the brain in 3D space is different, so we usually end up co-register one's reconstruction result (from our pipeline) with oneself T1.nii (come from mri_convert T1.dcm) so the structural mri reconstruction and dwi dcm files are in the same coordinate and can overlay. My understanding is that there is no coordinate tagged to ?h.sphere.reg files in 3D space, rather they are regulatory files which include some information about x,y,z vertices in regard to the surface of a hypothetical sphere (and the xyz are coming from the curvature of one's brain). As a result, I can use ?h.sphere.reg files as they are without any need to make any changes to match my files after they are coregistered. Is my understanding correct? I'm sorry if my language is not clear enough. I tried my best to describe the situation, but I'm not sure if my description is clear enough. Thank you for your help and time. Ela

2 4

Help with Pass Code to open Freesurfer on Virtual Machine
by Tatevosyan, Ellen 27 Jul '22

27 Jul '22

External Email - Use Caution Hello, I am a neuroimaging researcher and have been trying to install Freesurfer on a Windows OS using a Virtual Machine, following the instructions below: "Download and Run the Virtual Machine: Ubuntu 18.04.06 compressed image with the Freesurfer 7.2.0 release installed: FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1PaZD_uN8-j2duK-8vB8-Bcab_yu4LfPOhhM0EQRGqACIp…> Right click on the <file name>.ova.7z file and see what options you have under the choices for "Open with". If your current archive program choices cannot open a 7zip file, then try installing one of the utilities listed below. You will be prompted for a pass code when the archive is successfully opened. If you do not have the pass code to open the image, then send an email to the Freesurfer help list to receive it." I do not have the passcode to open the image and therefore am emailing the freesurfer help list, please advise. Best, Ellen Tatevosyan ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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Re: [Freesurfer] Recon-all Error
by gianrocco 27 Jul '22

27 Jul '22

External Email - Use Caution Hi, I attache hereby my email, as it was rejected — since I was not registered yet to the list Thanks again Kind regards, Gianrocco Lazzari, PhD Data Scientist Bottneuro AG Novartis Campus Lichtstrasse 35 CH-4056 Basel http://secure-web.cisco.com/17Y2qSzhq15HxclrMA69XhvYHw2lGCrZENRbQDKRbHm2V3n… > On 26 Jul 2022, at 14:52, gianrocco <gianrocco.lazzari(a)bottneuro.ch> wrote: > > Dear FreeSurfer support, > > > I am trying to test free surfer, via simNIBS , following this tutorial > > https://secure-web.cisco.com/1YEzvCpyUjM2PMRYydvY1jHKmlqYlJ-JWWr1Xh3Hl4PJvP… <https://secure-web.cisco.com/1YEzvCpyUjM2PMRYydvY1jHKmlqYlJ-JWWr1Xh3Hl4PJvP…> > > > It gets stuck at recon-all — please, find attached the relevant logs files > > Thanks for your support > > Ps: On Ubuntu 20.04.4 LTS and FS 6.0 > > <mri2mesh_log.html> > <recon-all.log> > <mri2mesh_test_output.txt> > > > Kind regards, > Gianrocco Lazzari, PhD > Data Scientist > > Bottneuro AG > Novartis Campus > Lichtstrasse 35 > CH-4056 Basel > > http://secure-web.cisco.com/17Y2qSzhq15HxclrMA69XhvYHw2lGCrZENRbQDKRbHm2V3n… <http://secure-web.cisco.com/12xOLcSIrJvEzOYEBbc5FdScOYhlzYDvpu048O9Ds8UprMP…> >

2 1

Group Analysis - FSGD and Contrast
by Boa Sorte Silva, Narlon 27 Jul '22

27 Jul '22

External Email - Use Caution Dear experts, I am conducting a group analysis and wanted to confirm that the set up below accurately addresses our research question. Thanks for your help, much appreciated! Background: * We have two groups (intervention vs control) and two timepoints (pre vs post) * Our data have already been processed and stacked with long_mris_slopes where pc1 is the measure of interest (post - pre). * Our covariates are sex (male vs female), age, and MMSE scores. * Thus, our model has 4 groups (2 factors/2 levels): * int_male * int_female * con_male * con_female * We’re using DODS * We’re running the analysis with mri_glmfit in the Longitudinal Two Stage Model As such, we want test whether there are greater changes in the intervention group vs control group in the pc1 measure, adjusting for the influence of sex, age, and MMSE. This is our FSGD: GroupDescriptorFile 1 Title Between-group Class int_male Class int_female Class con_male Class con_female Variables age mmse Input 001.MR int_male 30 25 Input 002.MR int_female 40 22 Input 003.MR con_male 60 29 Input 004.MR con_female 60 21 … And this is the contrast matrix +0.5 +0.5 -0.5 -0.5 +0 +0 +0 +0 +0 +0 +0 +0 With the above contrast matrix, our interpretation would be: * Intervention > control = positive result * Intervention < control = negative result Is this the correct set up and interpretation? Thanks for taking the time, Best regards, Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon[X]

2 2

Surface-based functional ROI analysis on both hemispheres at once
by Andy Kim 26 Jul '22

26 Jul '22

External Email - Use Caution Dear FreeSurfer Team, Hi. I am writing this email to ask if there is any way to do functional ROI analysis from both hemispheres at the same time, but not separately. My research question is to investigate visual hierarchy system under certain fMRI tasks using surface-based analysis. I am not interested in differences between hemispheres. There was the same question previously (https://secure-web.cisco.com/1n5iUWdnTAoX8uAScZjw9vgkzDWKHItczK2oXOxDKgvBSj…) but the answer didn't help. What I understand from the post is that I can do ROI analysis on both hemispheres just like I do it on one hemisphere. But that didn't work for me. If I can't do ROI analysis on both hemispheres at once, can I get mean beta values from ROI on each hemisphere, add them together and divide by 2 to get the average beta value? This is what I have done: # merge lh and rh labels mri_mergelabels -i lh.wang2015atlas.V1d.label -i lh.wang2015atlas.V1v.label -i lh.wang2015atlas.V2d.label -i lh.wang2015atlas.V2v.label -i rh.wang2015atlas.V1d.label -i rh.wang2015atlas.V1v.label -i rh.wang2015atlas.V2d.label -i rh.wang2015atlas.V2v.label -o lhrh.wang2015atlas.V1d+v+V2d+v.label # GL is the project name. funcroi-config -label lhrh.wang2015atlas.V1d+v+V2d+v.label -analysis GLanalysis.rh -roi rhlh.wang2015atlas.V1d+v+V2d+v.roicfg funcroi-sess -sf GLsublist -roi rhlh.wang2015atlas.V1d+v+V2d+v.roicfg funcroi-table-sess command showed an error "ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when the label and surface are from different subjects or hemispheres or the surface has been changed since the label was created." The command showed no error with -anlysis GLanlaysis.lh option. My original plan was to compare results between -anlysis GLanalysis.lh and -anlysis GLanalysis.rh to see if they are the same. In addition, since the atlas is surface-based, I assume I cannot use -anlysis GLanalysis.mni305. “You must specify an analysis to use. The analysis (-analysis) space must match that of the anatomical ROI space. Ie, if the anatomical ROI is defined by a surface annotation, then the analysis must be a surface-based analysis. If the anatomical ROI is defined in the volume using a segmentation or a volume label, then the analysis must be volume-based (ie, mni305 or native).” from https://secure-web.cisco.com/16alnLo11o_FBGyXyWW5_UeEPfQq5ZPaNTtjI1ZVKmT8jr… The attached files are the output from funcroi-sess with different hemispheres options. What should I do for doing ROI analysis from the both hemispheres at once? Thank you in advance. Kind Regards, Andy (Junghyun) Kim

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BV/CSF index and Sulcal CSF
by Michele GRASSO 26 Jul '22

26 Jul '22

External Email - Use Caution Hello FreeSurfer Developers, My name is Michele Grasso and I am a student of the master's degree course in Computer Engineering at the University of Catania (Italy). I am interested in calculating the BV/CSF index [1] which is equal to the ratio between the sum of the volumes of gray matter and white matter and the volume of the CSF. Regarding the volume of gray and white matter, I referred to the TotalGrayVol and CerebralWhiteMatterVol volume statistics reported in the aseg.stats file. CSF volume was considered as the sum of two contributions: ventricular (Left Lateral Ventricle (SegId 4) + Left Inferior Lateral Ventricle (SegId 5) + Right lateral Ventricle (SegId 43) + Right Inf Lateral Ventricle (SegId 44) + 3rd Ventricle (SegId 14) + 4th Ventricle (SegId 15) + 5th Ventricle (SegId 72) + Right choroids plexus (SegId 63) + Left choroids plexus (SegId 31)) and sulcal CSF. I searched the list and the sulcal CSF is not segmented by Freesurfer as it is indistinguishable from bone on a T1-weighted MRI. What parameters in the aseg.stats file to consider to have a more likely measurement of the sulcal CSF? Could eTIV-BrainSegVolNotVent-ventricular volume be a good approximation? Finally, do I have to take into account the CSF statistic reported in the aforementioned file or ignore it completely? Thank you, Michele Grasso [1] https://secure-web.cisco.com/1M1Uy0HamoR49lrEsTneq1jOPjK14iKS2n5o_4kld4AC5H…

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Re: [Freesurfer] SynthSR: Illegal Hardware Instruction
by fsbuild 26 Jul '22

26 Jul '22

External Email - Use Caution Andrew might have a better way to do this, but you could try the following. Below you should substitute your base path to the freesurfer distribution for where /Applications/freesurfer/dev is used. 1) Setup your freesurfer environment with FREESURFER_HOME and source the setup script, e.g. zsh/bash, $ export FREESURFER_HOME=/Applications/freesurfer/dev$ source $FREESURFER_HOME/SetUpFreeSurfer.sh... output showing environment deleted ... 2) Download the tensorflow package, tensorflow-2.4.1-py3-none-any.whl, via the link, e.g. into $HOME/Downloadshttps://drive.google.com/file/d/15Qeve5FIA137KON67ehKIOyXy1N0PbAC/view?usp=sharing 3) Uninstall the existing tensorflow, $ sudo -H /Applications/freesurfer/dev/python/bin/python3 -m pip uninstall tensorflow 4) Install the downloaded tensorflow (this example assumes it is in your default Downloads folder = $HOME/Downloads). $ sudo -H /Applications/freesurfer/dev/python/bin/python3 -m pip install $HOME/Downloads/tensorflow-2.4.1-py3-none-any.whl 4) Check you have fspython in your path.  Then test the import succeeds and exit.$ which fspython/Applications/freesurfer/dev/bin/fspython$ fspython>>> import tensorflow... output deleted ...>>> ^D On Jul 25, 2022, at 11:27, Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote:Unfortunately, tensorflow and M1 don’t mix well at the moment. Not sure if there is a universal fix yet. Rob, do you remember where the mac-specific TF package can be installed from? Best,Andrew From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Abdelkarim, Ahmed <a.karam@ucl.ac.uk>Date: Tuesday, July 12, 2022 at 9:29 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] SynthSR: Illegal Hardware Instruction        External Email - Use Caution        Hello I have an issue getting SynthSR working with FreeSurfer dev.I have MacBook Pro with apple M1 chip and MacOS Monterey. In bash terminal, after setting up FreeSurfer, and running the SynthSR command, I get this error ‘’Illegal instruction: 4’’. Have you had a similar issue before? Any advice? Many thanks in advance. RegardsAhmed

1 0

mri_jacobian: what are the correct files to list as arguments?
by Danielle Carrol 25 Jul '22

25 Jul '22

External Email - Use Caution Hello, I am trying to compute the Jacobian for use in VBM. I found the following command on the email archive: mri_jacobian <3d morph> <template volume> <output volume> I am assuming the 3d morph is the file mri/transforms/talairach.m3z, since this file provides the nonlinear warp. However, I am confused about which file should be the "template volume". Is this the final transformed/registered volume for each subject (i.e. ${SUBJECTS_DIR}/<subject name>/mri/brain.mgz)? Is it the fsaverage template $FREESURFER_HOME/subjects/fsaverage ? I am using version 6.0.0. Thank you, DC PhD Student University of Wisconsin-Madison

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