[Freesurfer] mri_glmfit and --mask

Hello everyone, I am trying to incorporate a binary FMRI mask into mri_glmfit. The problem is that it does not matter what I put in for the mask file I get the same results. This is the command I am using: mri_glmfit \ --y /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/y.mgh \ --

[Freesurfer] Red Hat Enterprise Linux 6?

Hi Surfers, I was wondering if FreeSurfer v5.1.0 (CentOS 4 x86 (64b)) or V5.X will work on Red Hat Enterprise Linux 6? The reason I ask is that the supercomputer at Brigham Young University is going through a major overhaul: changing the OS, adding more nodes, and adding more storage. I am just

[Freesurfer] Error on Step 3 of longitudinally process

Hi, I was wondering if I am doing something wrong when doing step 3 of the longitudinally process. The error I get is: ERROR: Template/base ID cannot be the same as a time point ID (in /shared/subjects/subjects/a-aut-v510/10022/base-tps) Here is the environment: freesurfer-Linux-

[Freesurfer] aseg.mgz looks worse after longitudinal processing on 5.1

Hi Surfers, I have done some Longitudinal Processing on a bunch of subjects and although the pial and white surfaces are looking good after the Longitudinal Processing, the  aseg segmentation for each subject is often looking much worse. I have a link to a sample screen grab to show you what I me

[Freesurfer] How do I use "Subject Exclusions" in qdec

Hello Surfers, I am trying to do a qdec analysis and I am working with several hundred subjects. I have my data divided up into different time points and a discrete factor called time. I would like to look at just time 1, then time 2, then time 3. I know how to exclude individual scans by right c

[Freesurfer] asegstats2table problem

Hello Surfers, Command: asegstats2table --skip --delimiter comma --common-segs --stats=lh.BA.stats --meas volume --tablefile V5vo-BA-lh.csv --subjectsfile=a.txt I am trying to create a table of "lh.BA.stats" values where all subject are listed in a.txt. asegstats2table tries to work however ther

Re: [Freesurfer] asegstats2table problem

-hemi lh --delimiter comma ... > > > On 05/02/2012 03:10 PM, Brain Apprentice wrote: >> Hello Surfers, >> >> Command: asegstats2table --skip --delimiter comma --common-segs >> --stats=lh.BA.stats --meas volume --tablefile V5vo-BA-lh.csv >> --subjectsfile=a.txt

Re: [Freesurfer] asegstats2table problem

gt; It's aparcstats2table, not asegstats2table > > > On 05/03/2012 02:19 PM, Brain Apprentice wrote: >> >> Thank you very much Dr. Greve. >> >> I must still be doing something wrong. >> >> When I try : asegstats2table --skip --common-segs --delimite

[Freesurfer] Odd behavior in aparcstats2table of FreeSurfer V4.3.1

Hello, I am trying to combine data from 2 different runs of aparcstats2table and I noticed that although all the columns are there the order of the columns are different. Has anyone else noticed this? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mg

[Freesurfer] Where are all the segmentation names explained?

Hello, Generally speaking the segmentation names are self explanatory like Left-Hippocampus or 5th-Ventricle. There are some segmentation's that I am not sure what they mean like ctx-lh-unknown or ctx-lh-bankssts. Is there any place I can go that would explain these few segmentation names? Is ther

[Freesurfer] mri_convert questions?

Hello, I was just wondering if there was a way in mri_convert to conform a MRI scan so that the output file is 16-bit? The reason I ask is that I am trying to create dual pipelines. One pipe for Freesurfer and the other pipe for SPM and it would be nice to use mri_convert to generate the data for

[Freesurfer] Missing posterior tip of posterior horn of lateral ventricle V4.01 vsV3.05

Hello, I was comparing the processing of the "bert" sample data on FreeSurfer V3.05 with V4.01 and I noticed that the posterior tip of posterior horns of lateral ventricles both sides were not counted as part of the lateral ventricles but as cerebral white matter in V4.01. Have I done something wr