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
IN
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 li
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 ipsilesion
ve/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
> > --streg xhemi/surf/lh.fsaverage_sym.sphere.reg
phere.reg
> >
> > ERROR: Option --src-label unknown
> >
> >
> >
> > On Fri, Mar 17, 2017 at 11:26 AM, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > please send command line
> >
> >
> > On 3/17/17 10:3
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 works fine, but the
> 2nd step f
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
___
e combined.
>
> 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, an
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 o
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 to
run tracula on the subject. The problem is, the combined file doesn't have
a bvals/bvecs file. When I try to use the origi
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 wrote:
> Try re-running recon-all -qcache for that subject and see if the error
> goes away
>
> On 05/11/2016 10:56 AM, Marissa Pifer wrote:
> > The erro
; 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 Pifer wrote:
>
> Here is ev
o) 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 on qdec -
> >
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 people
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
ollected
> 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 input the command
gt;
> 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
>>
>> "Checking for (invalid) multi-
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!
/Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri
old computers? What is on the new one? Have you tried running
> the same data on each to get comparable timings?
>
> cheers
> Bruce
>
> On Mon, 28 Dec 2015, Marissa Pifer wrote:
>
> Hi Freesurfers,
>>
>> I've recently downloaded free surfer onto a new computer
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 wo
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