Dear Anastasia and Tracula users,
I ran the longitudinal pipeline of Tracula with my subjects and I finished
without error. However, I just realized now that I only added cingulum
gyrus ending but not the angular bundle. I am interested in tracts that
passes through hippocampus so angular bundle s
Thanks Douglas!
1 - I have two functional files per subject (.mgh). Is it possible to insert
two files per subject in mris_preproc? In my former functional analysis I
haven't concatenated my data using a FSGD-file when running mris_preproc.
2 - Can you calculate the difference between two func
Hello,
I need to process a good few thousand T1 images on a machine that I can't store
all the data on. I'd like to transfer as few files as possible to the
processing machine so that I can perform longitudinal processing. I have
successfully longitudinally processed some patients with a sub se
Hi,
Yes, we have permission, and the disk have plenty of space :/
On Thu, Mar 3, 2016 at 6:30 PM, Douglas N Greve
wrote:
> Do you have write permission to that folder? Is the disk full?
>
> On 03/02/2016 11:12 AM, Óscar Soto Angona wrote:
> > Hello,
> >
> > We are medicine students who are usi
Dear Freesurfer team,
Forgive me if this is a foolish question...
I wanted to overlook cortical thickness, area and volume measures in Gnumeric
file after recon-all (checking edits made). However, for several subjects I
noticed that the values of mean thickness (final column) were calculated wr
what if you change the destination directory? Does it work?
On Fri, 4 Mar
2016, Óscar Soto Angona wrote:
Hi,
Yes, we have permission, and the disk have plenty of space :/
On Thu, Mar 3, 2016 at 6:30 PM, Douglas N Greve
wrote:
Do you have write permission to that folder? Is the disk fu
hello experts
i have some question to you
Question 1.
i want to compare two groups(patients group VS control groups) for cortical
thickness asymmetry.
so.. am i using a lh.thickness.fsaverage.mgh and
rh.thickness.fsaverage.mgh for each group subjects right..?
Question 2.
Left hemisphere whole v
usually if the thickness is 0 that means that the vertex is not part of
cortex, typically because it is on the "medial wall" (adjacent to
ventricle) or in the hippocampus or some other non-neocortical structure
On Fri, 4 Mar 2016, A-reum Min wrote:
hello experts
i have some question to you
Q
for asymmetryc, see
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 03/04/2016 09:28 AM, A-reum Min wrote:
> hello experts
>
> i have some question to you
>
> Question 1.
> i want to compare two groups(patients group VS control groups) for
> cortical thickness asymmetry.
> so.. am i using a lh
Hi Ahearn,
the base needs a few files from all cross time points for processing. An
individual -long run needs files from the base and from *all* cross
time points. What is needed and how the stream works is described on the
wiki although that may not be complete, especially in situations wit
Hi,
I can't help you with ANOVA (never done that), but you can
- either subtract the two time points and then do a regular group analysis
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
- or run a Linear mixed effects model
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsM
Hi Marmaduke
I think there are some tools around for downsampling the surfaces like
mris_decimate. Have you tried any of them?
cheers
Bruce
On Wed, 2 Mar 2016, marmaduke woodman
wrote:
> Hi
>
> I would like to resample the cortical surface on the sphere at a lower
> resolution, and then deflat
Dear all,
I am working on calculation of cortical thickness from a set of subjects. I
am following the instructions from
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I
am able to run up-to step-2 successfully i.e. I can display the ROIs on
fsaverage subject volume. But
Hi
On 03/04/2016 07:06 PM, Bruce Fischl wrote:
> I think there are some tools around for downsampling the surfaces like
> mris_decimate. Have you tried any of them?
Yes, indeed mris_decimate works well for the downsampling.
However, I'd like to recover the cortical parcellation for the
downsam
On 03/04/2016 09:10 PM, marmaduke woodman wrote:
> However, I'd like to recover the cortical parcellation for the
> downsampled surface.
I tried to decimate the pial & white surfaces, generate a corresponding
thickness file and then
mris_sample_parc -ct /opt/freesurfer/FreeSurferColorLUT.txt tv
what are you trying to achieve? It might be easiest to use something like
fsaverage5 as the downsampled surface. Then you would just map your
subjects to fsaverage5 using the existing sphere.reg files
cheers
Bruce
On Fri, 4 Mar 2016, marmaduke woodman wrote:
> On 03/04/2016 09:10 PM, marmaduke
On 03/04/2016 10:06 PM, Bruce Fischl wrote:
> what are you trying to achieve?
A per-subject ~10k vertex pial surface with a corresponding annot. We
use it as a spatial domain for simulating neural activity; 150k vertices
is too many for this purpose.
> It might be easiest to use something like
I think you can map it to fsaverage5 then use mri_surf2surf with
-sval-xyz to map the fsaverage5 surface back to each subject
On Fri, 4 Mar
2016, marmaduke woodman wrote:
> On 03/04/2016 10:06 PM, Bruce Fischl wrote:
>> what are you trying to achieve?
>
> A per-subject ~10k vertex pial surface w
Dear. Freesurfer experts.
Hi. How are you?
It might be very naive question.
When using version 4.5.0 I used the command:
mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino
However under the version 5.3.0, mkbrainmask-sess does not have -funcstem.
May I use -maskstem in
Hello again,
To calculate cortical thickness, I am running step-4 & 5 following the
instructions from
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
So running step 4:
*mri_surf2surf --s S01_LP --trgsubject fsaverage --hemi lh --sval
lh.thickness --tval lh.thickness.fsave
In a simple word, my question is:
under version 5.3.0, how can I specify funcstem (stem of functional
volume)? I don't see any argument for that..
Thanks a lot.
Best,
Ji Won
2016-03-04 16:31 GMT-05:00 Ji Won Bang :
> Dear. Freesurfer experts.
>
> Hi. How are you?
>
> It might be very naive que
On 03/04/2016 10:19 PM, Bruce Fischl wrote:
> I think you can map it to fsaverage5 then use mri_surf2surf with
> -sval-xyz to map the fsaverage5 surface back to each subject
This seems to generate a surface with the number of vertices in the
subject, (160k) not fsaverage5 (10k), though perhaps I'
On 03/04/2016 10:50 PM, marmaduke woodman wrote:
> On 03/04/2016 10:19 PM, Bruce Fischl wrote:
>> I think you can map it to fsaverage5 then use mri_surf2surf with
>> -sval-xyz to map the fsaverage5 surface back to each subject
Sorry for the noise, fwiw, this seems to do the trick:
mri_surf2surf
The functional stream changed a lot from version 4 to version 5. The
commands and workflow are very different now
On 03/04/2016 04:31 PM, Ji Won Bang wrote:
> Dear. Freesurfer experts.
>
> Hi. How are you?
>
> It might be very naive question.
>
> When using version 4.5.0 I used the command:
> mkb
You specify it when you run mkanalysis-sess
On 03/04/2016 04:36 PM, Ji Won Bang wrote:
> In a simple word, my question is:
>
> under version 5.3.0, how can I specify funcstem (stem of functional
> volume)? I don't see any argument for that..
>
> Thanks a lot.
>
> Best,
> Ji Won
>
> 2016-03-04 16:
Thanks for your help!
I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0
What I used to run are:
mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino
inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd
bold_retino
However, since version 5.3.
sure, glad to hear it worked
Bruce
On Fri, 4 Mar 2016, marmaduke woodman wrote:
> On 03/04/2016 10:50 PM, marmaduke woodman wrote:
>> On 03/04/2016 10:19 PM, Bruce Fischl wrote:
>>> I think you can map it to fsaverage5 then use mri_surf2surf with
>>> -sval-xyz to map the fsaverage5 surface back to
Run preproc-sess instead. inorm-sess is no longer used
On 03/04/2016 05:18 PM, Ji Won Bang wrote:
> Thanks for your help!
>
> I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0
>
> What I used to run are:
> mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd
> bold_reti
Dear guys,
I was doing group analysis (command-line) on two groups (patients and
control, no age or other information). The data has been "qcached", and
after following the three steps as "mris_preproc, mri_glmfit and
mri_glmfit-sim" shown in the tutorial on the Freesurfer website, I obtained
the
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