[Freesurfer] tracula error message

Hi Freesurfers, Could you help me interpret this error message? I am attempting to run TRACULA using version 6 on a MacBook Pro OS X El Capitan Version 10.11.3 helpdesks-MacBook-Pro-2:R01_DTI crc$ trac-all -prep -c dmrirc.example1 INFO: SUBJECTS_DIR is /Users/crc/Documents/myprojects/R01_DTI

[Freesurfer] bvals and bvecs for tracula v6

Hi freesurfers, I recently updated my freesurfer version from 5.3 to 6, and I'm running into a problem with the tracula dmrirc.example file. In the dmrirc.example file for v5.3, it required just the bvals and bvecs in a text file in the correct format. For v6, it now requires a bval files, bval

[Freesurfer] Analyzing xhemi results

Hi free surfers, I have run the xhemi process on the subjects for my study. The study is on stroke patients and their lesions are a mix of left and right hemispheres. In analyzing the results, we want to look at correlations between fmri activation in M1 and the cortical thickness of M1

Re: [Freesurfer] xhemi label

mr.mgh.harvard.edu/safelinks/greve/mris_apply_reg > > > On 03/17/2017 11:47 AM, Marissa Pifer wrote: > > > > Marcs-MacBook-Pro:SRMC01-1 marchaut$ mris_apply_reg --src-label > > label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label > > --st

Re: [Freesurfer] xhemi label

reg > > > On 03/17/2017 11:47 AM, Marissa Pifer wrote: > > > > Marcs-MacBook-Pro:SRMC01-1 marchaut$ mris_apply_reg --src-label > > label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label > > --streg xhemi/surf/lh.fsaverage_sym.sphere.reg > > sur

Re: [Freesurfer] xhemi label

<gr...@nmr.mgh.harvard.edu> wrote: > please send command line > > On 3/17/17 10:38 AM, Marissa Pifer wrote: > > Hi freesurfers, > > I am using xhemi to map the right hemisphere of each subject to the left > hemisphere of the same subject. The first xhemi command

[Freesurfer] xhemi label

Hi freesurfers, I am using xhemi to map the right hemisphere of each subject to the left hemisphere of the same subject. The first xhemi command works fine, but the 2nd step for mapping the label, I get this error: "Option --src-label unknown" Do you know how to fix this? Marissa

Re: [Freesurfer] Getting combined bvals/bvecs

; Hope this helps, > > a.y > > > On Wed, 14 Sep 2016, Marissa Pifer wrote: > > Hello freesurfer experts, >> I am trying to run tracula on subjects that have separate AP/PA direction >> DTI files. We combined the data >> into one using topup, and would now like t

[Freesurfer] How to get numerical r values from analysis

Hi freesurfer experts, I've run into a problem of not being able to generate the numerical results of the analysis I've run through qdec.After I ran the analysis in qdec I opened the overlay in tksurfer, applied a label, and found a significant negative correlation between cortical thickness and

Re: [Freesurfer] QDEC - cannot allocate memory

That fixed the error. Thank you so much for your help! Marissa Pifer On Wed, May 11, 2016 at 11:32 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > Try re-running recon-all -qcache for that subject and see if the error > goes away > > On 05/11/2016 10:56 AM, M

Re: [Freesurfer] QDEC - cannot allocate memory

0.fsaverage.mgh > --o deleteme.mgh > mri_concat > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-2.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > --o deleteme.mgh > ... > > and see if there is one that generates the error > > > > On 5/11/16 9:15 AM, Marissa Pif

Re: [Freesurfer] QDEC - cannot allocate memory

about 3-4 years ago) we would see > that error because some of our files got corrupted. Can you send more of > the terminal output? > > On 05/10/2016 12:56 PM, Marissa Pifer wrote: > > Hi freesurfers, > > > > I am on a macbook pro OSX 10.9.5, trying to run an analysis o

[Freesurfer] QDEC - cannot allocate memory

Hi freesurfers, I am on a macbook pro OSX 10.9.5, trying to run an analysis on qdec - freesurfer version 5.3. I am looking to analyze T2weighted scans for 27 subjects through the qdec system. I keep getting this error that it cannot allocate memory for the task. I'v been talking with our IT

[Freesurfer] bvals bvecs Error

Hi freesurfers, I'm having a problem the bvals and bvecs for one of my subject's DTI data. When I try to run the first step of tracula I get this error message: "Error: data and bvals/bvecs do not contain the same number of entries" I have checked, the bvals and bvecs do contain the same amount

Re: [Freesurfer] Multiple Frames Error

? I would check with whoever collected > the data and get it sorted out before diving into an analysis. > > On 02/22/2016 02:34 PM, Marissa Pifer wrote: > > Bruce, > > > > I'm not sure why it has multiple frames. It was a spin echo, T1 > > weighted structural MRI. I inp

Re: [Freesurfer] Multiple Frames Error

-nth 0 two_frames.mgz 001.mgz > > Bruce > > > On Mon, 22 Feb 2016, Marissa Pifer wrote: > > Hi freesurfers, >> I am trying to run the recon-all command on a T1 weighted structural >> image for one of my subjects and I keep getting this error >> >> &quo

[Freesurfer] Multiple Frames Error

Hi freesurfers, I am trying to run the recon-all command on a T1 weighted structural image for one of my subjects and I keep getting this error "Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!

[Freesurfer] Recon-all Run Time

Hi Freesurfers, I've recently downloaded free surfer onto a new computer. It's working correctly, but the running time for the recon-all -all command is 30-50 hours. This is in contrast to when I've used free surfer on previous computers where the run time was 6-12 hours. I'm wondering why this