Re: [Freesurfer] function that do the same step like qcache?

Dear Bruce, I try to execute this command to smooth and resample data but I have one message of error: mri_surf2surf --srcsubject s000_open_brain_sanlm_+TIR_normlalized --srcsurfval curv --src_type curv --trgsubject avg_all_subjects_SD --trgsurfval curv --hemi lh --fwhm-src 15 --trg_type

[Freesurfer] Validation of results

Dear freesurfer users, I would really appreciate if anybody could confirm that I have preformed my analysis correctly as I have very little experience with freesurfer and I want to make sure that my result is a true finding. Firstly, I am looking at the effect of a schizophrenia risk variant on

Re: [Freesurfer] function that do the same step like qcache?

Hi Fatma try giving it the full path to the curv file. I think curv is the right format to specify, but I believe it needs the full path to the src and target cheers Bruce On Tue, 30 Jul 2013, fatma zribi wrote: Dear Bruce, I try to execute this command to smooth and resample data but I

Re: [Freesurfer] function that do the same step like qcache?

Hi Bruce, thank you very much it works! With best regards, Fatma 2013/7/30 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Fatma try giving it the full path to the curv file. I think curv is the right format to specify, but I believe it needs the full path to the src and target cheers

[Freesurfer] Deformed tksurfer results

Hi, I ran tksurfer (with the inflated surface option) on a couple of my subjects that had a major deformation in their orig.mgz file and the inflated surface of tksurfer looked as if a chunk was missing off of it at the position where the deformation is located. Is that normal? I have attached

Re: [Freesurfer] Unsegmented ventricles

Hi victor If you upload the subject I will take a look. 5.3 may help Bruce On Jul 30, 2013, at 1:36 PM, Victor Kovac kovac...@umn.edu wrote: Dear Freesurfer experts, I am running recon-all on very atrophied brains with mixed results. Attached is an image of a brain where segmentation has

[Freesurfer] funcroi-table-sess error

Dear Doug and Freesurfers, I am attempting to run funcroi-table-sess on a set of subjects but keep getting an error message I've never seen before: funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg -sf

[Freesurfer] Using gcut multiple times

Hello, Is there any value in running recon-all with -gcut multiple times? e.g. in a case where skull/dura continues to be left on brainmask.mgz? Thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Unsegmented ventricles

Bruce, I have uploaded it via file drop. The subject's name is MPS3021-4. Thanks, Victor On Tue, Jul 30, 2013 at 1:32 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: via ftp or file drop:

Re: [Freesurfer] Deformed tksurfer results

Hi Panos, you probably want to get a neuroradiologist to look at that scan. cheers Bruce On Tue, 30 Jul 2013, pfot...@nmr.mgh.harvard.edu wrote: Hi, I ran tksurfer (with the inflated surface option) on a couple of my subjects that had a major deformation in their orig.mgz file and the

Re: [Freesurfer] are many *.dat files written out to disk in subj_dir/mri and then deleted when autorecon completes?

Hi I did not find any DIAG environment variable. The situation is quite reproducible and really problematic as there are so many files written out. There are 75,776 dat files (at least in the case I report below). At least for part of them they appear to be batched in groups of 128 (0-127) and

Re: [Freesurfer] are many *.dat files written out to disk in subj_dir/mri and then deleted when autorecon completes?

Hi Albert I think I foundit. Do you have the envronment variable DEBUG defined? If so, remove it before running recon-all and these files will no longer be written. cheers Bruce On Tue, 30 Jul 2013, Montillo, Albert (GE Global Research) wrote: Hi I did not find any DIAG environment

Re: [Freesurfer] Deformed tksurfer results

Hi Bruce, I'm sorry, I didn't phrase the question correctly. I do know why the orig.mgz comes out like that, however, I don't now why does the inflated surface in tksurfer look as if a chunk is missing out of it. Thanks again, Panos Hi Panos, you probably want to get a neuroradiologist to

[Freesurfer] Cerebellar parcellation

Dear Freesurfers, I would like to perform cerebellar parcellation on structural mri with freesurfer. I asked if this was possible 6 months ago (see message below, saying that this feature wasn't available for now). I checked on freesurfer wiki the release notes about Freesurfer version 5.2.0

[Freesurfer] GLM Analysis: ROI (--label)

Hi FreeSurfer users, I am running a GLM analysis on the command line, and would like to look specifically within an ROI. I added the flag: --label lh.orbitofrontal.label, in my case, to mri_glmfit, but keep getting an error. It seems that whenever it hits this line in the command, it quits. If I

Re: [Freesurfer] Cerebellar parcellation

Hi Charles, The new cortical/cerebellar/striatum parcellations are derived from the resting-state fMRI data averaged across 1000 subjects in MNI152 space. If your subjects have already been warped to MNI152 space, then you can simply use those parcellations (which are in the

Re: [Freesurfer] GLM Analysis: ROI (--label)

what is your command line? Also, send the terminal output. On 7/30/13 6:41 PM, Rachel Jonas wrote: Hi FreeSurfer users, I am running a GLM analysis on the command line, and would like to look specifically within an ROI. I added the flag: --label lh.orbitofrontal.label, in my case, to