[Freesurfer] mritotal for talairach registration in FS7

External Email - Use Caution This email was sent 22 hours ago, but somehow it haven't appeared on the forum yet. I post it again. Gabor Perlaki ezt írta (időpont: 2021. jún. 2., Sze, 12:11): > The default talairach registration is wrong in ~20% of our subjects and > thus eTIV is

[Freesurfer] freesurfer-7.1.1 :: mcparams2reg is python2 script

External Email - Use Caution Hello, While installing freesurfer-7.1.1 for centos via rpm (freesurfer-CentOS8-7.1.1-1.x86_64.rpm) I had the following problem: /usr/local/freesurfer/7.1.1-1/bin/mcparams2reg is a python script that use /usr/bin/env python, not fspython which is 3

[Freesurfer] freesurfer-7.1.1 :: show_tal ::mri_show: Command not found

External Email - Use Caution Hello freesurfer-7.1.1 installed from rpm on centos8 show_tal tries to call mri_shown a non existing program in /usr/local/freesurfer/7.1.1/bin     regards     Eric ___ Freesurfer mailing list Freesurf

[Freesurfer] freesurfer-7.1.1 :: rebuild_gca_atlas.csh :: missing subjects.csh

External Email - Use Caution subjects.csh is not installed but rebuild_gca_atlas.csh requires it     best regards     Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinf

Re: [Freesurfer] freesurfer-7.1.1 :: show_tal ::mri_show: Command not found

External Email - Use Caution Le 03/06/2021 à 14:54, Eric Deveaud a écrit : > External Email - Use Caution > > Hello freesurfer-7.1.1 installed from rpm on centos8 > > show_tal tries to call mri_shown a non existing program in > /usr/local/freesurfer/7.1.1/bin     tal_co

Re: [Freesurfer] freesurfer-7.1.1 :: mcparams2reg is python2 script

External Email - Use Caution Le 03/06/2021 à 13:46, Eric Deveaud a écrit : > External Email - Use Caution > > Hello, > > > While installing freesurfer-7.1.1 for centos via rpm > (freesurfer-CentOS8-7.1.1-1.x86_64.rpm) I had the following problem: > > /usr/local/freesurfer/

[Freesurfer] freesurfer-7.1.1 "" anatomiCutsUtils :: missing lzma python module

External Email - Use Caution Hello, freesurfer-centos8-7.1.1 rpm installa in singularity container Singularity> anatomiCutsUtils -h /usr/local/freesurfer/7.1.1-1/python/packages/pandas/compat/__init__.py:117: UserWarning: Could not import the lzma module. Your installed Python i

Re: [Freesurfer] error at 3d normalization pass 1 of 2 stage with MP2RAGE data

External Email - Use Caution Hi Bruce, I am just following up on this. Were you able to get mri_normalize to run on this mp2rage data? Thanks, Corinna On Wed, May 5, 2021 at 6:50 PM Corinna Bauer wrote: > Great, thanks. The nu.mgz is attached. > > Corinna > > On Wed, May 5, 20

Re: [Freesurfer] freesurfer-7.1.1 :: mcparams2reg is python2 script

External Email - Use Caution Le 03/06/2021 à 15:53, Eric Deveaud a écrit : > External Email - Use Caution > > Le 03/06/2021 à 13:46, Eric Deveaud a écrit : >> External Email - Use Caution >> >> Hello, >> >> >> While installing freesurfer-7.1.1 for centos via rpm

[Freesurfer] Labels #601-#628

External Email - Use Caution Hello Experts, I am trying to isolate ROIs using labels #601-#628 however I am getting the following output and it is the same for each label. Any idea what is wrong here? Thanks for your help! Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.

Re: [Freesurfer] Recon-all running on a loop

Hi Diana, If there are a lot of obvious holes in the surface topology, it might be worth doing some manual fixing of the white-matter segmentation. The tutorial at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 walks through that process. Best Andrew From: DIANA ORT

Re: [Freesurfer] Tracula registration failure

Hi Marena - If the registration between the diffusion and T1 images is reasonable, this should work. You should bypass any pathways that lie mostly in the truncated part of the diffusion scans. Best, Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on be

Re: [Freesurfer] Error/shifting in cortical parcellation

Can you try an experiment for me? cd $SUBJECTS_DIR/subject/surf cp lh.sphere.reg lh.sphere.reg.auto # make a backup mris_register -norot -rotate 0 0 +15 -curv rh.sphere $FREESURFER_HOME/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif rh.sphere.reg Then run recon-all -s subject -autor

[Freesurfer] nalysis of covariance between functional connectivity data (FS-FAST) and cortical thickness

External Email - Use Caution Hi, how can I perform vertex by vertex (surface) analysis of covariance between functional connectivity data (FS-FAST) and cortical thickness, regressing out the effect of groups? My mean concern is how buid the fsgd file. Stefano__

[Freesurfer] Cortical Thickness Measures for MTL

External Email - Use Caution Hello, I have been manually tracing the entorhinal cortex, dividing it into the antero-lateral entorhinal and posterior-medial entorhinal cortex. I am looking for a way to get cortical thickness measures for this region. I have a few questions relat