Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

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

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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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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 this email archive (Re: [Freesurfer] Jacobian mri_cvs_register (mail-archive.com)<https://secure-web.cisco.com/1LenU0lNm3dfOywG0njDPZc5l9fJtDrLhnstVxKLgojhf4…>: 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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segment_subregions stats files missing?
by Alvarado, Luis 25 Jul '22

25 Jul '22

External Email - Use Caution Hi all, I ran the segment_subregions thalamus --cross on some of my subjects but I cannot find the *.stats files in the stats folder. I was wondering if I am missing something? I need the *.stats files to aggregate the results via asegstats2table to feed the mri_glmfit tool. Is there another way to do this without the *.stats files? I am using the freesurfer-linux-ubuntu20_x86_64-dev-20220716-015eeb0 build on Ubuntu 20.04.4 LTS. Best, Luis

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SynthSR: Illegal Hardware Instruction
by Abdelkarim, Ahmed 25 Jul '22

25 Jul '22

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. Regards Ahmed

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Failed to sign in
by krystaly 25 Jul '22

25 Jul '22

External Email - Use Caution Dear FS experts, I'm using FS 7.2.0 on ubuntu 18.4.6, which is running on Windows 10. However, when I entered the password that I received doesn't let me sign in. Would you please kindly advise? Thanks. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Re: [Freesurfer] Qdec: Can't find a usable init.tcl
by fsbuild 24 Jul '22

24 Jul '22

External Email - Use Caution Hello Rosa, The qdec program is deprecated in 7.X releases and is no longer maintained. In the 7.X releases, you can try using freeview for images and from the command line there are the mri* commands (mris_surf2surf, mri_glmfit, mri_glmfit-sim, etc.) for stream processing. If you still need to run qdec in the Freesurfer 6 distribution, then you could ask your IT department to create a virtual machine or container to host an older copy of your linux OS that supports the correct version of tcl/tk for Freesurfer 6.X and install the Freesurfer 6 distribution in it.   Linux has quemu for built in virtualization which you may already have installed on your server(s).  There is also docker for containers and VirtualBox for virtual machines which likewise can run an older version of an OS and run Freesurfer 6 in those.  Your IT group may support docker and/or VirtualBox as well. - R. On Jul 24, 2022, at 14:41, Rosa de los Angeles Tanzi <tanzi(a)cbs.mpg.de> wrote:       External Email - Use Caution        Dear FreeSurfer Developers,I'm attempting to open Qdec on my linux server. I used to open it with freesurfer 6.0.0 activated to analyze our local gyrification index data. That version is not available anymore in our service; hence, the Freesurfer version I can use is 7.1.0 and when I tried to open Qdec the following message appears: Can't find a usable init.tcl We tried to contact our IT sever to see if there was a way we could use our old Freesurfer version 6.0.0 (which we used to calculate the LGI). But they replied to us with the following:"A G6 compute server must be used for freesurfer 6.0.0.. The background is that the TCL 8.4.6 used by Freesurfer is very old (from 2008) and is no longer supported by current operating systems. The same applies to the latest version 7.2.0.We have TCL 8.6.11 available."Is there anyway we can install Qdec for this new version of freesurfer 7.1..0? so we are able to continue with the analysis. I am open to any other possible solutions.Kind regards,Rosa_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Qdec: Can't find a usable init.tcl
by Rosa de los Angeles Tanzi 24 Jul '22

24 Jul '22

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to open Qdec on my linux server. I used to open it with freesurfer 6.0.0 activated to analyze our local gyrification index data. That version is not available anymore in our service; hence, the Freesurfer version I can use is 7.1.0 and when I tried to open Qdec the following message appears: Can't find a usable init.tcl We tried to contact our IT sever to see if there was a way we could use our old Freesurfer version 6.0.0 (which we used to calculate the LGI). But they replied to us with the following: "A G6 compute server must be used for freesurfer 6.0.0. The background is that the TCL 8.4.6 used by Freesurfer is very old (from 2008) and is no longer supported by current operating systems. The same applies to the latest version 7.2.0. We have TCL 8.6.11 available." Is there anyway we can install Qdec for this new version of freesurfer 7.1.0? so we are able to continue with the analysis. I am open to any other possible solutions. Kind regards, Rosa

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(no subject)
by Danielle Carrol 21 Jul '22

21 Jul '22

External Email - Use Caution Hello, I am trying to compute the Jacobian for use in VBM. I found the following command on this email archive (Re: [Freesurfer] Jacobian mri_cvs_register (mail-archive.com)<https://secure-web.cisco.com/1qsFwf44rr-eT9vRJ1SxsVMe3116pQYdJVNi9THejnTrxk…>: 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/orig.mgz)? Or is it the fsaverage template $FREESURFER_HOME/subjects/fsaverage ? Thank you, DC PhD Student University of Wisconsin-Madison

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