Dear Freesurfers,
I am new to freesurfer and I am trying to understand how to best perform a
cortical thickness analysis for an ROI that is not pre-defined in
freesurfer, such as the IFJ or V5. Should I create a surface ROI label
using tksurfer (or freeview) or should I create an ROI in volume spa
Hi Bruce,
no, but do you mean by the entire subject directory?
Thank you so much,
regards,
E.
On Fri, Nov 20, 2015 at 1:45 PM, Bruce Fischl
wrote:
> Hi Elisabetta
>
> we would need the entire subject directory. Did you look at the surfaces
> I suggested?
>
> cheers
> Bruce
> On Fri, 20 Nov 2015,
Hi Elisabetta
we would need the entire subject directory. Did you look at the surfaces
I suggested?
cheers
Bruce
On Fri, 20 Nov 2015, Elisabetta del Re wrote:
> Hi Bruce,
> thank you so much.
> I attach here T1 of 2 of the cases.
> Thank you again,
> regards,
> Elisabetta
>
> On 11/4/15, Bruce
did you look at the help?
On 11/20/2015 01:21 PM, Sherihane Bensemmane wrote:
> mris_volmask can't work with my data ( error:
> mghRead(/data/fmri_monkey_raw/fs/subjects//thelma_anat5/mri/aseg.mgz, -1):
> could not open file), we can't with the anatomical images we have proceed to
> the regular
look at them in freeview
9 dof means 9 degrees of freedom in the registration, 3 translation, 3
rotation, and 3 scale. The 3 scale may account for errors in the voxels
size of the ct
On 11/20/2015 12:54 PM, Borzello, Mia wrote:
> Are any of the CT scans for this patient okay? How can I check? Th
mris_volmask can't work with my data ( error:
mghRead(/data/fmri_monkey_raw/fs/subjects//thelma_anat5/mri/aseg.mgz, -1):
could not open file), we can't with the anatomical images we have proceed to
the regular segmentation, we skip automatic segmentation because it wouldn't
work for monkeys.
So
I WAS able to replicate the error within the virtual machine
environment, but not on a standard Linux machine.
It looks like 'mri_glmfit-sim' command is not compatible with 32bit
freesurfer linux environment. My immediate recommendation is to simply
move past the error since the tutorial data c
Are any of the CT scans for this patient okay? How can I check? The one I
picked is 1 mm so I thought it was fine. Also, what does 9 dof refer to?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N
no. use --mkmask
On 11/20/2015 12:51 PM, Sherihane Bensemmane wrote:
> if i use mri_surf2vol on the pial alone, i would have the entire gray matter?
>
> Best regards,
> Sherihane Bensemmane
> PhD Student,
> Research Group Neurophysiology,
> K.U. Leuven,
> O&N II Herestraat 49 - box 1021
> 3000 Leu
The CT itself has incorrect parameters for the pixel size. You can try
using 9 dof instead of 6, but in the end you'll want to fix your CT probably
On 11/20/2015 12:47 PM, Borzello, Mia wrote:
> Hi Freesurfers,
>
> I am trying to coregister with a high-res CT, but for some reason am
> getting a
if i use mri_surf2vol on the pial alone, i would have the entire gray matter?
Best regards,
Sherihane Bensemmane
PhD Student,
Research Group Neurophysiology,
K.U. Leuven,
O&N II Herestraat 49 - box 1021
3000 Leuven, Belgium
From: freesurfer-boun...@nmr.mg
you can try mris_volmask or mri_surf2vol. volmask is the better choice
if it works for your data. Look in recon-all to see how to call it. This
is what creates the ribbon.mgz file, which sounds like what you need
On 11/20/2015 12:28 PM, Sherihane Bensemmane wrote:
> Hi,
> I am using freesurfer f
Hi Freesurfers,
I am trying to coregister with a high-res CT, but for some reason am getting a
very sheered image when I am in tkregister. Should I use another CT?
Thank you!
1) MG93
2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig
3) no error message, just a sheer
Hi,
I am using freesurfer for non_human primate. I did the segmentation in
freesurfer , at the end i have the wm.mgz but not grey matter since the command
to get it during segmentation doesn't work in monkey brain. in the forlder
/surf/ i have all files such as lh/rh.pial, curv, sulc, white. Sin
Hi Bruce,
thank you so much.
I attach here T1 of 2 of the cases.
Thank you again,
regards,
Elisabetta
On 11/4/15, Bruce Fischl wrote:
> Hi Elisabetta
>
> I don't think that's an error, just a warning. That said, a defect with
> 38K vertices is awfully big, almost 1/4 of the surface, which usually
Hi Lisa,
for a subject with N time points, you will have 2N+1 directories:
Stage1: N cross sectionally (independently) processed
Stage2: 1 base/template, representing average anatomy of this subject
Stage3: N longitudinally processed subject that use some joint
information from the cross (stage
Hi Doug,
when I try to execute mri_coreg, I get the following error message:
error while loading shared libraries: libnetcdf.so.6: cannot open shared
object file: no such file or directory
Caspar
2015-11-19 18:49 GMT-05:00 Douglas Greve :
>
> Can you try mri_coreg instead of fsl?
> ftp://surfe
Ok, i actually think it would be easier to have only one FS version. How could
i get the BA labels (and all the other coontents of fsaverage) again?
Best,
Max
On dijous 19 novembre 2015 15:51 CET, Bruce Fischl
wrote:
> yes, that's pretty much it. Alternatively we could just give you a
Hi,
I would like to know if, in doing a longitudinal study (i.e. 2 or 3 MRI
each subjects), this is usual to have many file for one subject (see the
picture, 5 file for one subject with two MRI : a0009_1 = MRI 1 and a0009_2
= MRI 2) ? Because in the future I will have around 100 subjects with 3 MR
19 matches
Mail list logo
