Thanks.
The maps produced in slope and intercept folders are very similar and opposite
in colors.
I have already applied this contrast but I think that they did not fit with my
goals.
Why the intercept did not produce the same results of G4VO?
The slope effect is very similar to the inverse of in
Dear All,
I designed an adaptive filter according to local gyrification index values
and then want to see the lgi histogram of new smoothed brain volume.
However freesurfer gave an error as:
ERROR: mritotal failed, see transforms/talairach.log
It seems that the input volume orientation has chang
Hi Chintan - Freesurfer is open source, so all of our source code is available,
but trac-all is actually a shell script, so you can find it under
$FREESURFER_HOME/bin/.
TRACULA just expects the output files of bedpostX, and does not care if they
were generated on GPUs or CPUs. Just provide the
Dear FreeSurfer users,
I am using Freesurfer 6.0 and Tracula 6.0 for processing MRI and DTI scans. The
second step of the trac-all pipeline performs the ball-and-stick fit with the
bedpost function from FSL. Documentation for FSL suggests that the use of GPUs
can considerably speed this process
Hi Christoph,
1) I would use only intercept as random effect. I like to keep the model simple
and - as you say - there is only a max of 2 time points. If you like you can do
a model comparison (see wiki page) to compare the two models.
2) I would use the exact time in years (as float with deci
Doug,
Sorry if I muddied things by going into the significant digits - accurate to 5
seems reasonable. I was simply meaning to say that the rotation and scaling
parameters are not the issue, to save the reader time inspecting them.
The translations (final three parameters) are off by anywhere 3
I don't know what might be going wrong here. Have you tried to re-run it
from scratch? Are you out of disk space?
On 10/16/17 12:59 PM, Yagmur Ozdemir 19 wrote:
I am using version 6.0.0 and this is made from scratch. Just a couple
of days ago I processed a different subject but used the specia
I am using version 6.0.0 and this is made from scratch. Just a couple of days
ago I processed a different subject but used the special retinotopy procedure
and didn't come across this problem. I first noticed this error in selxavg-sess
and went back and used mkbrainmask, register-sess and prepro
I don't know what coordinates those are. Can you give indices? indices
are non-neg
On 10/16/17 12:59 PM, Nicholas Goh wrote:
An example of the aparc+aseg not covering all that it needs to can be
found around [-7, 114, 133]
On Mon, Oct 16, 2017 at 12:47 PM, Douglas Greve
mailto:gr...@nmr.mgh
You have to do it one hemi at a time, eg,
mri_surf2vol --hemi lh --so lh.bp.nii.gz --subject fsaverage --o
smoothed.bpnd.in.volume.nii.gz
mri_surf2vol --hemi rh --so rh.bp.nii.gz --subject fsaverage --merge
smoothed.bpnd.in.volume.nii.gz --o smoothed.bpnd.in.volume.nii.gz
On 10/16/17 12:5
An example of the aparc+aseg not covering all that it needs to can be found
around [-7, 114, 133]
On Mon, Oct 16, 2017 at 12:47 PM, Douglas Greve
wrote:
> what is the index (ie, col, row, slice) where you are seeing a problem?
>
> On 10/16/17 11:44 AM, Nicholas Goh wrote:
>
> Hi,
>
> I am not su
Got it, thanks! I have already performed smoothing on the MGX surfaces so I’d
like to proceed with mri_surf2vol.
According to the “hidden secrets of success” for mri_surf2vol, there are 2
methods. Is the command below correct?
mri_surf2vol --so lh.bp.nii.gz (the PET surface BPNDs) --so rh.bp.n
I don't think you can use the mris_label2annot ctab. What happens if you
run freeview using the default ctab?
On 10/10/17 3:19 PM, Sims, Sara A wrote:
Freesurfer people,
*I have a label file that I want to make into a volume file only in
the white matter to use in diffusion tractography.*
what is the index (ie, col, row, slice) where you are seeing a problem?
On 10/16/17 11:44 AM, Nicholas Goh wrote:
Hi,
I am not sure if this email got lost in the process or is still
awaiting approval, but I was asked to tar and gzip the images that I
was having no luck with fixing the white
You can
mri_binarize --gm --i aparc+aseg.mgz --o gm.mask.mgz
On 10/16/17 12:41 PM, Elijah Mak wrote:
Hi Doug,
I am looking for a total GM mask that includes cortical and
subcortical regions.
Best Wishes,
Elijah
*Dr. Elijah Mak, Research Associate
*Department of Psychiatry
Old Age Psychiat
Hi Doug,
I am looking for a total GM mask that includes cortical and subcortical regions.
Best Wishes,
Elijah
Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities
Research Group
University of Cambridge
Trinity
Not sure I understand. If the two transforms are only off by less than
the 5th decimal, then why are the registrations off so much. As for why
it would be off at the 5ht dec, it probably has to do with the way we
store the matrix. When a volume is read in, the matrix is decomposed
into translat
Sorry, try this
mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label
--streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
On 10/13/17 2:58 PM, Neuro Lists wrote:
Hi all,
I was just wondering if there was any further insight into what I
might be doing wrong on this.
they all look ok except that these should be
C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
On 10/13/17 11:30 AM, std...@virgilio.it wrote:
> I have applied the contrasts that we discussed in the previous mails but they
> produc
I'm not sure what you mean/want. If you run preproc-sess with the
-mni305 flag, it will resample to mni305 space and mask out
non-subcortical structures
On 10/12/17 11:14 AM, Jan Willem Koten wrote:
Normalize to mni
Dear Doug,
We have a very simple question. In a first step we segmented br
May the ROI to the surface using mri_vol2surf, then use mri_segstats to
extract the mean value
On 10/13/17 4:09 PM, Dev vasu wrote:
Dear all,
I have a ROI mask volume file and i would like to generate Mean
cortical thickness surface file (i.e lh.ROI.thickness.fsaverage.mgh
and rh.ROI.thic
which version of FS are you using? Is this a new analysis done from
scratch or had you preprocessed before?
On 10/15/17 4:10 PM, Yagmur Ozdemir 19 wrote:
Hello Freesurfer experts,
After I run preproc-sess with this command (
preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s
Interesting.. would you mind sending me the command you ran and file drop the
input and output volumes to me?: https://gate.nmr.mgh.harvard.edu/filedrop2/
Emma
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fereshte
Sent: Sunday, October 15, 2017
run the juelich atlas through recon-all, then use mri_vol2surf
On 10/14/17 3:38 PM, Dev vasu wrote:
Dear all,
I have custom ROI mask ( MNI Space ) that i have prepared from Jülich
atlas , I would be like to obtain corresponding surface label file,
Could you please guide me necessary the st
that includes GM regions. not sure what you want
On 10/13/17 8:58 PM, Elijah Mak wrote:
Hi Doug,
That subcort mask is only GM (sorry, should have indicated that when
I named it).
I just looked at the subcort mask in the cvs 2mm folder and it looks
like it is only subcortical? I am looking
it comes down to have you smooth it. If you do it in the volume, then
you need to smooth it in the volume, and that is an invalid analysis
with MG.
On 10/13/17 8:42 PM, Elijah Mak wrote:
> Hi Doug,
>
> I wonder what is the difference between this approach (mri_surf2vol) as
> opposed to doing t
Dear Everyone,
My lab has new openings for postdoctoral fellows. Please see job
descriptions here: https://yeolab.weebly.com/jobs.html
Thanks,
Thomas
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do you really want the atlas in MNI space or do you want an individual
subject parcellation mapped to MNI? If the atlas, I think it already is, or
at least it lives on the fsaverage surface which has associated MNI coords.
Doug can confirm.
cheers
Bruce
On Mon, 16 Oct 2017, cain
wrote:
Th
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