I'm still not sure why you are trying to do this. If FSL did not unpack
the volumes with the correct orientation, then you need to switch to
mri_convert. If they are in the right orientation, then I don't
understand what you are trying to do.
doug
On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
>
Hi Doug,
After the coregistration failed for the majority of the subjects, I visually
inspected a handful of the subjects in freeview and it looks like the
anatomical and the functional are reversed but I could be wrong.
The nifti files are unpacked from DICOMs using unpack_fsl.sh
(/cluster/
Dear Friends,
I have used a mixed set of images from 1.5T and 3.0T scanners with anisotropic
voxel size in my study. I used Freesurfer tools for converting them to
isotropic voxel size before segmentation and reconvert to initial state after
segmentation. It is appreciated if someone let me kno
That sounds fishy. I would use the 5.3 or 6.0 version.
On 08/16/2016 03:51 PM, miracle ozzoude wrote:
> FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
>
> On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> What version of FS (
FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve
wrote:
> What version of FS (and mri_mcsim) are you using? Does it die if you run
> with just a few reps (eg, 100)?
>
> On 08/16/2016 01:21 PM, miracle ozzoude wrote:
> > Hello Fr
which ROIs are coming up zero? Have you looked at the area maps for that
subject for that ROI?
On 08/16/2016 01:16 PM, A Nunes wrote:
> I mean the area of an ROI
>
> On Tue, Aug 16, 2016 at 6:59 AM, Douglas N Greve
> wrote:
>> please include previous correspondence. Do you mean the area of a ver
What version of FS (and mri_mcsim) are you using? Does it die if you run
with just a few reps (eg, 100)?
On 08/16/2016 01:21 PM, miracle ozzoude wrote:
> Hello FreeSurfer team,
> While running monte carlo correction with 1 reps (mri_mcsim) for
> the whole hemisphere, I received this error at
How do you know that the structural is left-right reversed? Or that the
fMRI is? How did you create the nifti files?
On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
> Hi,
>
> I'm having trouble co-registering a bunch of subjects whose T1 is
> left-right reversed. While the orientation of the stru
On 15 August 2016 at 19:21, Karamfil Bahchevanov wrote:
> I'd like to experiment with faster proceesing, in fact I'd like to try CUDA.
> However there are several possible drivers for my quadro K2000. I'm not sure
> which one to choose. Should I install the latest 7.5. version, or use the
> older
Hi,
I'm having trouble co-registering a bunch of subjects whose T1 is left-right
reversed. While the orientation of the structural file in the NIfTI header is
LIA and the orientation of the functional volume is LAS, visual inspection
shows that the structural is left-right reversed. I then foll
Hello FreeSurfer team,
While running monte carlo correction with 1 reps (mri_mcsim) for the
whole hemisphere, I received this error at 975 reps for the left hemisphere
" 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216) failed
(error code=12)
*** error: can't allocate region
*** set
I mean the area of an ROI
On Tue, Aug 16, 2016 at 6:59 AM, Douglas N Greve
wrote:
> please include previous correspondence. Do you mean the area of a vertex
> or the area of an ROI?
>
> On 08/15/2016 06:06 PM, A Nunes wrote:
>> Hi Douglas,
>>
>> I meant a surface area extracted from a surface bas
please include previous correspondence. Do you mean the area of a vertex
or the area of an ROI?
On 08/15/2016 06:06 PM, A Nunes wrote:
> Hi Douglas,
>
> I meant a surface area extracted from a surface based atlas.
>
> Thanks
> Adonay
> ___
> Freesurfer
Hello Lee,
Opensuse platforms versions greater than 12.1 are not compatible with the
FreeSurfer licensing scheme, but their are workarounds. I will contact you
offline so we can figure out the best solution for your setup.
-Zeke
> Hi,
> Our IT department have recently upgraded our cluster OS a
Dear developers,
I was wondering if you could let me know how can I extract a table for the
measure pial_lgi.
Best wishes,
Vasiliki
Vasiliki Chatzi, BA(Hons) MSc
PhD student | Department of Psychosis studies
Institute of Psychiatry, Psychology and Neuroscience | King's College London
_
Hi Nick,
it looks like the base finished without error. But if your *.long.basid/surf/
are missing the lh.thickness , then something went wrong when processing the
-long runs. I would recommend to run a single subject step by step to see what
goes wrong (could be IO problems or disk space etc).
Hi Han,
there is two things going on here.
1. for some reasons there are small differences in the acquisition parameters
across your time points. This usually indicates that there was a change in
protocol wich could bias your longitudinal study (depending on what was changed
and if this is co
Hello FS's experts,
Would anyone have an advice for my problem ?
Best regards,
Matthieu
2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte :
> Dear experts,
>
> I am in trouble with two ways of computing mean intensity with
> mri_segstats.
>
> First I have used on .annot files with three different l
Hi
I looked at the distribution areas with almost zero thickness and when
I saw they were on one hemisphere, I checked my bash script and found
out that for the left cortex it was calling the right hemisphere
areas.
However, I still have a few subjects which have zero thickness in some
areas of my
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