Thank you very much for your kind answer.
Mohamed
On 18/02/16 23:22, Bruce Fischl wrote:
> The ex vivo is probably more accurate since it was created by directly
> visualizing the relevant cytoarchitectur
>
>> On Feb 18, 2016, at 5:17 PM, Douglas N Greve
>> wrote:
>>
>> One (aparc) is derived
I have also run as followed but the error persist.
mri_convert $SUBJECTS_DIR/Subj2/MRS_Voxel_FS_space.nii.gz
$SUBJECTS_DIR/Subj2/mri/MRS_MASK2.mgz
mri_convert $SUBJECTS_DIR/Subj2/MRS_Voxel_FS_space.nii.gz MRS_MASK2.mgz
fcseed-config -segid 1 -seg MRS_MASK2.mgz -fsd rest -mean -cfg MRS_MASK2.
On Thu, 18 Feb 2016, Z K wrote:
> > is there a public clone of freesurfer on github?
> Sorry, their is no public freesurfer on github. But at the current
> moment (and forseeable future) the public repo is an exact mirro of the
> private repo.
> > --disable-GUI-build -- wouldn't it disable t
Hello,
sorry for asking this again
I want to calculate the difference between the thickness of one subjects
different hemispheres and show this on pial (left or right or even
fsaverage_sys). so I have ran :
surfreg --s $subject --t fsaverage_sym --lh
surfreg --s $subject --t fsaverage_sym --lh -
What is your mris_preproc command line? If you run mris_preproc with
--xhemi, it should give you two frames (left hemi and right hemi). If
you want to compute left-right, then add --paired-diff to the command
line. The output will be on the lh of fsaverage_sym. This can be
displayed on the whit
I think so. Just make sure you don't try to draw conclusions from the
ROI or area around it.
On 2/19/16 2:02 AM, amirhossein manzouri wrote:
Yes, I extracted the mean thickness of the ROI label from each
timepoint to use it as a continuous variable and study the correlation
of whole brain thic
Thank you very much for your prompt response.
However, I am doing the same analysis (with Repeated Measures ANOVA 2x2) in
different MRI acquisitions, so I would like to do the same analysis in
freesurfer.
Could you please help me?
Thank you,
Best regards,
Maria.
2016-02-18 23:22 GMT+01:00 Doug
Of course. Just another question to make sure I understand your answer
correctly. What you suggested with the fsgd file and contrast is the same
as running Qdec on the two time points as two groups and ROI as variable in
the dec table and then select the ROI as continuous and group as discreet
with
Hi,
I'm analyzing a decision making task with a 3x3 condition matrix: pairings of
low, medium, high levels of risk with low, medium, high levels of reward.
I've set up the following FSGD file to do a repeated measures/within-subject
ANOVA:
GroupDescriptorFile 1
Class hc001
Class hc002
Class hc
Dear FreeSurfer experts,
I would like to use the P. Hagmann atlas (Lausanne 2008 available here
https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs) on my
subjects. I ran Recon all on their T1 images and then these two commands
to get the Hagmann parcellation for my subject:
mris_
right
On 2/19/16 10:48 AM, amirhossein manzouri wrote:
Of course. Just another question to make sure I understand your answer
correctly. What you suggested with the fsgd file and contrast is the
same as running Qdec on the two time points as two groups and ROI as
variable in the dec table and
On 2/19/16 11:00 AM, Thomas Jacquemont wrote:
> Dear FreeSurfer experts,
>
> I would like to use the P. Hagmann atlas (Lausanne 2008 available here
> https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs) on my
> subjects. I ran Recon all on their T1 images and then these two comman
Make sure that the MRS_MASK.mgz itself has some voxels with value=1, and
make sure that there are enough of them to fit into at least one
functional voxel.
Make sure that the registration is accurate.
When you run run fcseed-sess, add -debug, capture the output, and send
it to me.
On 02/18/
Yes, that is expected given your command line.
On 02/18/2016 06:52 PM, std...@virgilio.it wrote:
> By running
> mri_cor2label --i $SUBJECTS_DIR/mri/MRS_MASK.nii.gz --id 1 --l MRS.label
>
> and opening the MRS.label by tksurfer fsaverage rh inflate -aparc -overlay
> MRS.
> label
> the inflate is e
Hello Yaroslav,
Ive built freesurfer on Debian "Jessie" platform. It was just a matter
of adding "libtool-bin" and "tcsh" to the list of packages that need to
be installed. Ive update the wiki page:
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
I still wasnt quit
I have been able to build the FS GUI tools succesfully on Ubuntu in the
past... Admittedly this was a long time ago (pre 14.04 days). I can dig
through my notes and see if they are still applicable. We no longer have
any Ubuntu 14.04 boxes -- we're currently on 15.10 ... which I suppose
in a fe
Ive discovered that if you add the following line to the
freeview/Makefile.am file then it will build succcessfully.
freeview_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS)
freeview_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS)
-freeview_LDFLAGS = $(QT_LDFLAGS) $(OS_LDFLAGS)
+freeview_LDFLAGS
Hi Douglas,
Sure! Below is the terminal outputs when I try and run the command you
suggested on the first five subjects. Any help you could provide would be
much appreciated!
Best,
LS
$asegstats2table --common-segs --meas volume --tablefile
/mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/
Hi Thomas
the seed sets the random number generator to the same starting point so
that the algorithm is repeateable.
Maybe Doug can comment on the second question. How are you visualizing it?
cheers
Bruce
On Fri, 19 Feb 2016, Thomas Jacquemont
wrote:
> Dear FreeSurfer experts,
>
> I would li
On Fri, 19 Feb 2016, Z K wrote:
> Hello Yaroslav,
> Ive built freesurfer on Debian "Jessie" platform. It was just a matter
> of adding "libtool-bin" and "tcsh" to the list of packages that need to
> be installed.
I had tcsh but not libtool-bin installed in that chroot... heh
> Ive update th
On Fri, 19 Feb 2016, Yaroslav Halchenko wrote:
> On Fri, 19 Feb 2016, Z K wrote:
> > I still wasnt quite able to get the freeview GUI to build. But If you
> > change the "--disable-GUI-build" flag to "--without-qt" then you will
> > get all the tktool GUIs except freeview. Im working on getti
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