[Freesurfer] f.nii & f.nii.gz compatibility

Hi, I am going to be running some new analyses on an old data set from another lab group that was collected in 2005/2006. Their group unpacked and analyzed using the f.nii.gz format; however, our lab unpacks and anayzes the f.nii format. Since I will be comparing the group from their lab w

Re: [Freesurfer] WM intensity normalization problem

couple of pictures of it, but I'm not sure how to do so in tkregister2. On Aug 17, 2009, at 5:40 PM, Bruce Fischl wrote: > wow, I haven't seen that before. Can you check the talairach.xfm > and see if it's correct? > On Mon, 17 Aug 2009, Garth Coombs wrote: >

Re: [Freesurfer] WM intensity normalization problem

ok at why our tal alignment code was not able to > handle this image. > > Nick > > > > On Tue, 2009-08-18 at 10:05 -0400, Garth Coombs wrote: >> When I check the talairach.xfm using tkregister2 --mgz --s >> amcg_anat -- >> fstal --surf orig, it does not extend

[Freesurfer] func2roi registration flag

Hi, We ran a data set through fslregistration, did our analyses, and then ran everyone through bbregister. We now want to do a new func2roi analysis using the fslregistration (so that it is consistent with our previous analyses). Is there a way to know which registration file (register.dat

[Freesurfer] isxconcat-sess error

Hi, I've been running into a problem when trying to run a group analysis. When I go to run isxconcat-sess, I use this command: isxconcat-sess -sf hc.txt -df sesspar -analysis Ext -c CS+lvsCS-l - percent -o ./HC-Ext-083109 -hemis -trgsubject fsaverage It runs through the whole isxconcat withou

[Freesurfer] fixing bad tal registrations

Hi, I recently ran into a problem with some of my tal registrations during the recon-all process (see below message to Martino's Tech). In order to fix the problem, it was suggested that we run bbregister outside of the recon-all stream and then feed that registration into the subsequent

Re: [Freesurfer] fixing bad tal registrations

. Does anyone have any advice on how to fix the registration? Thanks, Garth > > -- > > On Tue, 16 Mar 2010, Garth Coombs wrote: > >> Hi, >> >> I recently ran into a problem with some of my tal registrations during the >> recon-all process (see below mess

[Freesurfer] label2label with two subjects directories

Hi Doug & Freesurfer experts, Is there a way to run mri_label2label to copy a label from one subject to another in a different SUBJECTS_DIR, or do the subjects have to be in the same directory for label2label to work (e.g. vs_subject1 in SUBJECTS_DIR_A to subject1_anat in SUBJECTS_DIR_B)? I am

[Freesurfer] ROI Analysis Discrepency

Hi Doug, I am running into a similar problem that Yuko describes in Martinos Tech message 5099 (wouldn't let me reply directly). Using Stable 4, I made an old analysis last spring and extracted ROI values, yielding significant differences between two conditions as expected. I believe I original

[Freesurfer] HippSubregions File Missing

Hi All, I tried a runnings some recons (one recon entirely in Stable 5.1.0 using the -hippo-subregions flag, and one recon in Stable 4.5.0 followed by "recon-all -hippo-subregions" in 5.1.0), and I am running into a small problem in that the posterior_Left-Hippocampus.mgz file does not seem to