Re: [Freesurfer] Hippocampal subfield segmentation

2011-07-12 Thread Koen Van Leemput
Hi Wayne, You're right: It will be difficult to somehow shoehorn the probability images with voxel size 0.5mm isotropic into the orginal 1mm isotropic FreeSurfer volumes. The other way around, by resampling the 1mm input image onto the correct 0.5mm grid is easy, though: kvlUpsample nu.mgz 2 kvl

[Freesurfer] QDEC thickness data to table

2011-07-12 Thread Alexandru Hanganu
Dear Freesurfer experts, In the QDEC plot there is the possibility to view cortical thickness for each subject in a specific region. Is there a possibility to make an automatic table of all these thickness data ? In a previous question, the answer was to use a script: ===

Re: [Freesurfer] Hippocampal subfield segmentation

2011-07-12 Thread Bruce Fischl
Or you could use freeview to display them as an overlay without any resampling. What is it you are trying to do? On Jul 12, 2011, at 5:56 AM, Koen Van Leemput wrote: > Hi Wayne, > > You're right: It will be difficult to somehow shoehorn the probability > images with voxel size 0.5mm isotropic

[Freesurfer] tkregister2

2011-07-12 Thread Ignacio Letelier
Hi freesurefers I tried to visualize my functional data using the command: tkregister2 --s --reg --fslreg --surf orig --tag and i received this error : ERROR: trying to convert FSL registration matrix to FreeSurfer, but FSLOUTPUTTYPE variable is not set. Can anyone help me with this , Than

[Freesurfer] (no subject)

2011-07-12 Thread 林鄞
Dear everyone, I just have a problem when installing Freesurfer. I can’t process the command of “tkmedit”. How can I solve this problem? Thank you! setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv FREESURFER_HOME opt/freesurfer s

Re: [Freesurfer] Hippocampal subfield segmentation

2011-07-12 Thread Wayne Su
Thank you Koen. We're investigating the VR Space volume in each hippocampal subfield. Your suggestion is just what I'm looking for, very helpful. Yes, I can use freeview to display them as an overlay. don't how freeview achieves that. Are you sure no resampling there for the command: freeview nu.m

Re: [Freesurfer] Error while loading qdec project file

2011-07-12 Thread Tetiana Dadakova
When the Load Project is run, nothing is created in /tmp/qdec_project_archive, and then the error appears in terminal window. The only files/folders I have in /tmp/qdec_project_archive are: fsaverage, QdecProjectMetadata.txt, Untitled (this is the folder named as my project), Version.txt. Thank yo

[Freesurfer] Question about mri_label2label

2011-07-12 Thread John Richey
Dear freesurfer experts, I have a question about the use of a registration matrix in the context of mri_label2label. I have a series of labels that were created through mri_volcluster (each significant cluster from a .sig map was saved as a uniqe label as a product of that command), and I wish to

Re: [Freesurfer] (no subject)

2011-07-12 Thread Krish Subramaniam
Hi Lin When you extracted the archive, did you encounter any errors? You seem to be following the right steps. Also check if the md5 sum is correct $md5sum freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz It should output ba9d374e611d7a22a4c484e333b60b4c (see http://surfer.nmr.mgh.har

Re: [Freesurfer] Hippocampal subfield segmentation

2011-07-12 Thread Bruce Fischl
it of course resamples for overlay, but it doesn't downsample - just uses the vox2ras matrices from the two volumes to compute a common space On Tue, 12 Jul 2011, Wayne Su wrote: > Thank you Koen. We're investigating the VR Space volume in each hippocampal > subfield. Your suggestion is just wha

Re: [Freesurfer] Hippocampal subfield segmentation

2011-07-12 Thread Wayne Su
Thanks. Does freeview use same approach as what Koen described? Look like both ways need upsampling nu to 0.5x0.5x0.5. Wayne On 12/07/11 10:29 AM, "Bruce Fischl" wrote: > it of course resamples for overlay, but it doesn't downsample - just uses > the vox2ras matrices from the two volumes to co

Re: [Freesurfer] (no subject)

2011-07-12 Thread Rudolph Pienaar
Lin, why are you putting 'sudo' in front of each command you are running? That is not necessary. In fact, there should be no need to run FS as root (which is what 'sudo' does). Also, depending on your setup, by typing 'sudo' you might in leave the FS environment for that command. Try your comma

[Freesurfer] Request for DICOMS

2011-07-12 Thread Satrajit Ghosh
hi, if you have pointers to publicly available DICOM data or willing to share such data publicly from different scanners and acquisition sequences for structural, diffusion and functional data from human participants, please contact me off list. currently, the more varied the scanners and sequenc

Re: [Freesurfer] Error while loading qdec project file

2011-07-12 Thread Nick Schmansky
try deleting the directory qdec_project_archive: cd /tmp rm -Rf qdec_project_archive then run the Load Project command in Qdec. n. On Tue, 2011-07-12 at 19:10 +0200, Tetiana Dadakova wrote: > When the Load Project is run, nothing is created in > /tmp/qdec_project_archive, and then the error a

[Freesurfer] tracula - fix bad bbregister's

2011-07-12 Thread GREGORY R KIRK
Hi, I processed about 80 subjects with -prep stage and then checked the bbregister registrations with tkregister2 --mov /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/dwi.nii.gz --reg /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/xfms/anatorig2diff.bbr.dat --surf foun