[Freesurfer] Split a lablemap in the .annot format into parts

Dear FS Community, is there an easy way to split a lablemap in the .annot format into parts? In detail I would like to split network 6 (frontoparietal) of the yeo atlas (fsaverage/label/rh.Yeo2011_7Networks_N1000.annot) into the frontal, parietal and temporal part on each side. Is there an easy

[Freesurfer] How to deal with different resolutions in recon all and hippocampal subfield segmentation

External Email - Use Caution Hi, I'm working on data from different sites, scanned with different MRI-Scanners ans slightly different parameters (all in the range of 1x1x1 to 1.2x1.2x1). I wonder if you would recommend to run recon all and segmentation of HC sub-fields in differen

[Freesurfer] mri_watershed Error

External Email - Use Caution When I run recon-all i get the follwing error message: mri_watershed Error: GLOBAL region of the brain empty ! Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-X

Re: [Freesurfer] mri_watershed Error

an you check to make sure that the input to the watershed looks ok? Also, in > general it is a lot easier for us to help if you send us the full command > line and screeen output and attach the recon-all.log > > cheers > Bruce > > > On Thu, 11 Oct 2018, Boris Rauchmann wr

Re: [Freesurfer] mri_watershed Error

rms dir) if you want and I'll take a look > cheers > Bruce > > > On Thu, 11 Oct 2018, Boris Rauchmann wrote: > >> External Email - Use Caution >> Hi again, >> >> sorry. Please find attached

[Freesurfer] cortical thickness calculation based on hammersmith segmentation

External Email - Use Caution <>Dear FreeSurfer Developers, I´m trying to extract the cortical thickness of individuals from a study cohort based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as a volumetric file. I already run recon-all on all subjec

Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

ller > description of exactly how it is not working? > > On 1/25/19 10:56 AM, Boris Rauchmann wrote: >> External Email - Use Caution >> >> <>Dear FreeSurfer Developers, >> >> >> I´m trying to extract the cortical thickness of

Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

rs_mith_atlas_n30r83_SPM5surf.mgh > > cheers > Bruce > > > On Sun, 27 Jan 2019, Boris Rauchmann wrote: > >> External Email - Use Caution >> Hi, >> I used the following commands: >> mri_vol2surf —src .../Hammers_mith_atlas_n30r83_SPM5.ni

[Freesurfer] -so unknown in mri_surf2vol?

External Email - Use Caution My_pc$ mri_surf2vol --o 0021_thickness-in-volume.nii.gz --subject 0021 \ --so $SUBJECTS_DIR/0021/surf/lh.white $SUBJECTS_DIR/0021/surf/lh.thickness \ --so $SUBJECTS_DIR/0021/surf/rh.white $SUBJECTS_DIR/0021/surf/rh.thickness ERROR: Option --so unkno

[Freesurfer] mri_coreg error

External Email - Use Caution Hi FreeSurfer community, when I run mri_coreg I get the following error. /XYZ/2123/mri/brainmask.mgz is in the specified location. Can you help me with this? Thanks! Boris mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta Could not set loca

[Freesurfer] PETSurfer and thickness data

External Email - Use Caution Dear FS community, I would like to assess how PET tracer uptake is related to thickness changes in AD patients. Is it possible to generate difference maps for both methods and run a GLM? Or would you suggest another approach? Thanks, Boris

[Freesurfer] recon-all error after maual control points definition

External Email - Use Caution reading input surface xyz/fs_all_subjects/0031/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface

[Freesurfer] (no subject)

External Email - Use Caution Dear Freesurfer community, I am trying to extract SUV values from sub-cortical segmentation or gtmseg I don t want to use any PVC. I used the following commands: gtmseg --s xyz then mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta fol

Re: [Freesurfer] (no subject)

gt; > In mri_segstats, use --seg $SUBJECTS_DIR/xyz/mri/aparc+aseg.mgz > --ctab-default ... > when you use --annot, you are saying that the input is on the surface. > > On 5/17/2019 9:07 AM, Boris Rauchmann wrote: >> External Email - Use Caution >> >&

[Freesurfer] PetSurfer gtmpvc

External Email - Use Caution Hi all, is there a way to easily get the volume stats for all regions after pvc correction using mri_gtmpvc ? I think its not included in gtm.stats.dat. Thanks, Boris ___ Freesurfer mailing list Freesurfer@n

[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

External Email - Use Caution Dear all, depends the Segmentation of hippocampal subfields and nuclei of the amygdala pipeline on the fs-recon all pipeline? I made some changes mainly by defining control points to fix intensity normalization in my dataset and rerun recon all. I´m

[Freesurfer] scan acquisition date from recon all

External Email - Use Caution Dear all, is there any way to find the scan acquisition date in the recon-all log? Thanks, Boris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

[Freesurfer] Group mean tracer uptake images

External Email - Use Caution Dear FS community, how can I create group mean tracer uptake images in surface space with FS from several overlays? Thanks, Boris Von meinem iPhone gesendet ___ Freesurfer mailing list Freesurfer@nmr.mgh.

[Freesurfer] (no subject)

External Email - Use Caution Dear all, my intention is to use the Brainnetome Atlas parcellation/segmentation in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used: gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab '/media/XYZ/BN_Atlas_freesurfer/

Re: [Freesurfer] (no subject)

nnetome is, but it looks like you have it in > annotation form. I think that command should work. Why are you using > --no-xcerseg? This will cause it to not include extracerebral > structures. Also note that you cannot use arbitrarily small segments > when doing PVC. > >

Re: [Freesurfer] (no subject)

on the shape as > well). > > I think the --no-xcerseg is the right way to go now > > On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Thank you for your prompt answer - the command worked. This is th

Re: [Freesurfer] (no subject)

er, the PVC > noise amplification will become bigger (it also depends on the shape as > well). > > I think the --no-xcerseg is the right way to go now > > On 8/13/19 11:00 AM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > Thank

Re: [Freesurfer] (no subject)

n > subcortical seg for the given subject > > On 11/5/19 1:06 PM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > I just realized that the above mentioned command (gtmseg --s XYZ --o > > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ct

[Freesurfer] Using individual atlas in PETSurfer

External Email - Use Caution Dear all, I have a LUT, a gca file for subcortical segmentation and two gcs files for parcellation available. How can I get SUVRs for both the cortical and subcortical structures? I tried using xcerebralseg to create a individual segmentation to repl

Re: [Freesurfer] (no subject)

structures, but only the subcortical would also be fine as long as I can get mri_gtmpvc running on it. Thanks, Boris On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019

Re: [Freesurfer] PETSurfer individual atlas for subcortocal segmentation

External Email - Use Caution Did you already have the time to look at the logfile? Do you have any suggestions how to proceed? Thank you! > Am 02.12.2019 um 19:18 schrieb Boris Rauchmann : > >  > In this example tried it with only the subcortical segmentat

Re: [Freesurfer] PETSurfer individual atlas for subcortocal segmentation

ately, I think this is > going to require a fair amount of effort on my part. When I wrote this part > of PETsurfer, I just did not make it super flexible. > doug > > > On 12/5/2019 10:17 PM, Boris Rauchmann wrote: > > External Email - Use Caution > Did you already

Re: [Freesurfer] (no subject)

N_Atlas_subcotex.mgz as input to xcerebralseg, and then > run gtmseg as you have done below. > > Let me know if that works > doug > > > On 12/2/19 1:18 PM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > In this example tried it with

Re: [Freesurfer] (no subject)

chl : > > Hi Boris > > can you send us the full command line and screen output of the commands that > are failing? > > cheers > Bruce > On Thu, 12 Dec 2019, Boris Rauchmann wrote: > >> External Email - Use Caution >> Thanks. unfortunately I ge

Re: [Freesurfer] (no subject)

> > On 12/12/19 12:57 PM, Boris Rauchmann wrote: > > > > External Email - Use Caution > > > > My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg > > BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz > > SUBJECTS_DIR /Users

Re: [Freesurfer] (no subject)

External Email - Use Caution Here the results: pwd: /Users/boris/Desktop/MirLIND_test/1122/mri ls -l BN_Atlas_subcotex.mgz: -rwxrwxrwx 1 boris staff 37013 13 Aug 23:30 BN_Atlas_subcotex.mgz Best, Boris > Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D. > : > > pwd _

Re: [Freesurfer] (no subject)

External Email - Use Caution Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): could not open file > Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. > : > > mri_info N_Atlas_subcotex.

Re: [Freesurfer] (no subject)

:12 schrieb Greve, Douglas N.,Ph.D. > : > > There is something weird about that file. How was it created? > doug > ps. Please include previous correspondence in the email > > On 12/16/19 1:12 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution

Re: [Freesurfer] (no subject)

: -1. -0. -0. 128. -0. -0. -1. 128. -0. 1. -0. 128. -0. -0. -0. 1. > Am 16.12.2019 um 21:21 schrieb Boris Rauchmann : > > Thanks, it was crea

Re: [Freesurfer] (no subject)

External Email - Use Caution Dear Douglas, I uploaded two files: 1122.tar.gz is the sample subject and BN_Atlas_freesurfer.tar.gz this is the Atlas I want use for the cortical and subcortical parcellation/segmentation. Thank you so much, Boris > Am 02.01.2020 um 17:06 schrieb

Re: [Freesurfer] (no subject)

n 12/12/2019 11:57 AM, Boris Rauchmann wrote: >> External Email - Use Caution >> >> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg >> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz >> SUBJECTS_DIR /Users/boris/Desktop/mydir &g

Re: [Freesurfer] (no subject)

_DIR/1122/mri when you run mri_aparc2aseg and are you sure that > BN_Atlas_subcotex.mgz is in the same folder? > >> On 1/3/20 3:07 PM, Boris Rauchmann wrote: >> >> External Email - Use Caution >> >> Thank you for testing it. As before I get the same e

Re: [Freesurfer] (no subject)

fs_all_subjects/BN_Atlas_subcortex.gca' --o BN_apas+head.mgz Any ideas on that? Best, Boris Am Mo., 6. Jan. 2020 um 23:14 Uhr schrieb Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu>: > Are you sure you have permission to view that file? > > On 1/6/20 5:01 PM, Boris Rauchmann

Re: [Freesurfer] (no subject)

External Email - Use Caution Thanks, that solution seems to work finally. I just ignored the remaining voxels labeled according to the standard aseg scheme and proceeded with the the PET analysis and the combined LUT. I will ignore the remaining fragment labels from the original

[Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

External Email - Use Caution Dear FS experts, In my dataset I have 4 subjects where the T1 was acquired, planning the FOV very close to the occipital lobe. I guess that triggers the error: getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7 slices behind head! ER

Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

External Email - Use Caution Please find the logfile attached. Thank you Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve < dgr...@mgh.harvard.edu>: > Can you send the log file? > > On 6/4/2020 9:12 AM, Boris Rauchmann wrote: > > Externa

Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

> It will ask you for a password: use "anonymous" (no quotes) > cd transfer/incoming > binary > put subject.tar.gz > Send an email that the file has been and the name of the file. > > > On 6/4/2020 9:40 AM, Boris Rauchmann wrote: > > External Email -

[Freesurfer] tkregisterfv -ss

External Email - Use Caution Dear all, is there a way to use freeviews -ss command to obtain snapshots using tkregisterfv? I have a bunch of registrations to check and would prefer to do that using a bash script and snapshots. tkregisterfv --mov template.nii.gz --reg template.re

[Freesurfer] PETSurfer

External Email - Use Caution Dear all, How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean intensity using PETSufer? Is there a command to use in mri_gtmpvc like --rescale X? I know that I can find the mean in global.gm.dat and I can use that value for sca

[Freesurfer] PETSurfer voxelwise statistic

External Email - Use Caution Dear all, How can I run a voxelwise statistic using grey and white matter uptake? mgx.ctxgm.nii.gz and the other files in output all only include gm as I understand. My goal is to run whole brain volume-based analysis. Like in this example for subcort