Thanks, Doug!
I think we were probably going about this the wrong way. If I transform the ROI
from MNI space back into native space, will the following commands give the
proper cortical thickness extraction from native space?
mri_vol2surf --mov roi_in_native_space.nii.gz --out rh.roi_in_native
and does that file exist in /tmp? Is there space in /tmp?
On 02/28/2018 01:33 PM, Yash Patel wrote:
> Yes, I made sure I had permission to write into /tmp.
>
> On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> do you have write permission to /t
Hello,
Thank you so much! I used the following command as you said and got an
error : must specify a source registration file or --regheader
mri_vol2surf --src negative_allsocial_avgnull.nii --src_type analyze
--trgsubject fsaverage --hemi lh --o ./neg_allsocial.nii --projfrac 0.5
Best,
Srishti
Hi Sarah,
Drawing an ROI on a surface is a little bit complicated. You will need
to have a surface and volume loaded first. Then you create or load a ROI
as a volume ROI. On the control panel, there should be a "Map to
surface" option, you can map the ROI to the loaded surface. Then you
shoul
Great! Thank you so much, Andrew.
I downloaded the updated Freeview. I am still wondering how to draw an ROI
on the surface in Freeview. I don't have the options.
Could you please let me know what command you are running to get the
Freeview?
I am having the updated version Jan 2018.
Thanks,
Sara
I would add that my guess is the FLAIR is helpful up to about 1.25-1.5mm
thickest dimension
cheers
Bruce
On Wed, 28 Feb 2018, Glasser, Matthew wrote:
> The trouble with highly anisotropic resolutions is that your resolution is
> only as good as your worst axis for the convoluted cerebral corte
Thanks for the advice. I did have permission to write into /tmp; however
the HPC wouldn't allow it through the mri_segstats command line.
The issue was resolved by making a directory in the tmp manually, and then
mri_segstats works normally.
Thanks,
Yash
On Wed, Feb 28, 2018 at 1:33 PM, Yash Pate
The trouble with highly anisotropic resolutions is that your resolution is
only as good as your worst axis for the convoluted cerebral cortex. 0.8mm
or better would be optimal given a minimum cortical thickness of 1.6mm.
You can always try with what you have and see if it is net beneficial or
not
Hi all,
I wonder if people have any data (or anecdotes - I'm not picky) with regard to
how high of resolution T2w or FLAIR images need to be in order to be useful for
FreeSurfer's pial refinement. I've seen a couple threads suggesting the optimal
is ~1mm isotropic, and that thick slice (1x1x5 m
Yes, I made sure I had permission to write into /tmp.
On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve wrote:
> do you have write permission to /tmp ?
>
>
> On 02/27/2018 03:25 PM, Yash Patel wrote:
> > Hello FreeSurfer experts,
> >
> > I am attempting to run "mri_segstats --annot [subjectid] l
can you tar or zip the data in
/Volumes/PPDrive/Alliance/Source/Cases2Resubmit/MissingFSoutput_20180222/CVCD03060383
and send it to me on our filedrop (see below)
On 02/27/2018 04:28 PM, Cheryl McCreary wrote:
>
> Dear Experts,
>
> I am trying to process a some T1 data through FreeSurfer 5.3.0, b
do you have write permission to /tmp ?
On 02/27/2018 03:25 PM, Yash Patel wrote:
> Hello FreeSurfer experts,
>
> I am attempting to run "mri_segstats --annot [subjectid] lh aparc
> --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035"
>
> Whenever I try, I receive the following e
what version of FS are you using?
On 02/27/2018 01:29 PM, shilin18 wrote:
>
> *Hi all, very nice to find a place to ask all the fs giants a question.*
>
> *I run recon-all …-all -localGI, which always return this at the end.
> Can anyone help me find out what I need to do to evade this error?
>
It would not work by default. I think it could be made to work, but it
would take a lot of work
On 02/28/2018 11:12 AM, std...@virgilio.it wrote:
>
> Hi list,
>
> I wonder to know whether the FS-FAST tool is applicable on High Res
> Hippo fMRI images (175x60x175mm; 0.39x2x0.39mm).
>
> In parti
Hi list,
I wonder to know whether the FS-FAST tool is applicable on High Res Hippo fMRI
images (175x60x175mm; 0.39x2x0.39mm).
In particular do you think that it could be possible to map the FC of a
subfiled with the rest of the hippocampus?
If yes, have you particular advises on this issue.
T
what is your contrast of interest? If you are interested in the age
slopes, then you don't need to demean. If you want to use age as a
nuisance variable, then you should first test for an interaction between
age and group using the DODS model. If there is no interaction, then
switch to a DOSS m
you need to add --trgsubject fsaverage to your mri_vol2surf command line
On 2/27/18 12:23 PM, srishti goel wrote:
Hello,
We are trying to project a volume map onto a surface. Our network
based volume map is a .vmp file and our surface is a nifti file. We
were able to convert the volume maps
You are currently using 6 dofs (rigid registration). If you use --dof
12, it will get better. Having said that, nothing will make it that good
since this is a volume-based affine registration.
On 2/28/18 10:04 AM, Albrecht, Daniel S. wrote:
Hi Doug,
Sorry for the lack of information. We are
Dear All,
We invite you to the " 1st International Workshop on Predictive Processing
(WoPP) " organized by Basque Center on Cognition, Brain and Language (BCBL)
that will be held in one of most beautiful cities in europe, San Sebastian,
Spain from 20 - 22 June 2018 , at Palacio Miramar in Don
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