Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

Hi Douglas, Thanks for the help! However, when I tried the --nofixmni flag, all the ROIs appeared to have identical MNI coordinates. I have pasted the output from 3 ROIS in the LH. # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZNVtxs 13.332 83949 82219.39-29.4

Re: [Freesurfer] cannot find qdec file

Hi Doug, this is the result it printed out in the terminal: etsch:/scr/etsch2/kids$ mris_preproc --debug --qdec-long long.qdec.table.dat set echo = 1 ; set debug = 1 ; set debug = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag =

[Freesurfer] Is the fsaverage in the MNI space?

Dear freesurfer experts, The freesurfer online manual stated that before group analysis, we should resample data onto the common space (fsaverage). I have three questions here. First, Is the fsaverage file in the MNI space? In some previous studies, they report significant clusters with MNI

Re: [Freesurfer] Label or Overlay of Surface files

Hello, I am trying to load surface overlays in 3D Slicer on top of surface meshes (e.g. lh.Inflated), but surface overlays somehow don't load properly into 3D slicer, I am trying right surface files (lh.sulc , lh.curve e.g.)? On Fri, Aug 7, 2015 at 10:14 AM, Saeed Mahdizadeh Bakhshmand

Re: [Freesurfer] registering 2 scans

Hi Bruce, My goal is to compare the surfaces and segmentations from the reconstructions of the images from the 2 head coils. I'd like to be able to visualize the surfaces from both scans/coils on the same structural image. Thanks, Matt From:

[Freesurfer] registering 2 scans

Hi Freesurfers, I've scanned the same subject with 2 different head coils and reconstructed the memprage's from each coil with freesurfer. I'd now like to register these two reconstructions to each other, both the volumes and the surfaces. I've generated an lta registration matrix using

Re: [Freesurfer] registering 2 scans

Hi Matt can you tell us what your goal is for this analysis? You could use the longitudinal tools depending on what you are up to cheers Bruce On Fri, 14 Aug 2015, Hibert, Matthew Louis wrote: Hi Freesurfers, I've scanned the same subject with 2 different head coils and reconstructed the

[Freesurfer] Trakula

Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found

[Freesurfer] mris_make_surfaces error

Dear Freesurfer experts, I'm trying to run *mris_make_surfaces* with a FLAIR.mgz file as input. I used the same command as used if I run autorecon3, in order to make a pial refinement. Here is the command: mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1

Re: [Freesurfer] Freesurfer Surface Loading Error

You have the most recent (i.e. development) version of freeview installed on top of the version 5.3 release of freesurfer. However, the development version of freeview has diverged to far from its original package, and is no longer compatible with freesurfer version 5.3. If you want to use

Re: [Freesurfer] mris_make_surfaces error

Hi Marc, You can try running this command, to complete all the steps in recon-all that use FLAIR images to improve your pial surfaces: recon-all -FLAIRpial -s subject_name Best, Lee On Fri, 14 Aug 2015, Marc Garriga Peguero wrote: Dear Freesurfer experts, I'm trying to run

Re: [Freesurfer] Label or Overlay of Surface files

SOLVED. On Fri, Aug 14, 2015 at 4:08 PM, Saeed Mahdizadeh Bakhshmand saeedbakhshm...@gmail.com wrote: Hello, I am trying to load surface overlays in 3D Slicer on top of surface meshes (e.g. lh.Inflated), but surface overlays somehow don't load properly into 3D slicer, I am trying right

Re: [Freesurfer] Label or Overlay of Surface files

Hi Saeed lh.sulc and lh.curv are scalar overlays, not surfaces. The surfaces are e.g. lh.inflated, lh.white, lh.pial, etc cheers Bruce On Fri, 14 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: Hello, I am trying to load surface overlays in 3D Slicer on top of surface meshes (e.g.

Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag

Hi again, Prabesh would you mind trying this? It was a suggestions from a Mathworks representative. Please edit $FREESURFER_HOME/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh and right under the line that says export XAPPLRESDIR;, please insert this line of code: JAVA_TOOL_OPTIONS If it

Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag

Sorry, I actually meant: unset JAVA_TOOL_OPTIONS Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Eugenio Iglesias e.igles...@bcbl.eu To: Freesurfer

Re: [Freesurfer] segmentation fault while running -hippocampal-subfields-T1 flag

Hi Eugenio, Thank you for your help. I saw your first email and tried running with JAVA_TOOL_OPTIONS and it worked. It is still running without segmentation fault. After I finish that one I will run with unset JAVA_TOOL_OPTIONS. I will let you know the result of second run. Regards, Prabesh

Re: [Freesurfer] Registering surface files from fsaverage_sym to individual subjects

Dear FS experts Thanks for your help. Just to let you know I had registered rh .mgh files to the lh of fsaverage_sym in order to calculate inter hemispheric differences (lh minus rh). So, in order to transform back, I need to firstly register the .mgh file back to the right hemisphere and