Hi everyone,
In an earlier post, I had asked how to transform the white surface of one
subject to the white surface of another subject, and Bruce Fischl suggested
mri_surf2surf should be able to do this. After looking over the website
material related to mri_surf2surf, I find I'm not sure how mr
Hi all,
I've used itksnap to make edits to the ribbon.mgz (which was first
converted to a nifti) file to fix the segmentations of several subjects and
I now want to use this file to recreate the surface and curvature files for
each subject so that I can make an average subject that uses these fixe
Sorry, I'm answering your emails in reverse order. Your command should
do what youwant once you use the new version below
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf.snowleopard
note the --tval-xyz requires an argument (give it the orig.mgz)
doug
On 08/30/2013
This comes out:
drwxrwxrwx. 1 root root 0 Aug 29 11:10 /mnt/hgfs/Linux_Share/subjects
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 201
Hi Doug!
I am using free surfer on a VM. The file system in the physical computer is
NTFS.
Thanks,
Katica
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent:
Hi Yoon
Yes, you can also analyze area that way.
Best, Martin
On 08/30/2013 04:47 PM, Chung, Yoonho wrote:
Thanks Martin!. I have another quick question.
I am also interested in looking at developmental changes in the brain during
adolescence period in normal subjects and also comparing our con
Thanks Martin!. I have another quick question.
I am also interested in looking at developmental changes in the brain during
adolescence period in normal subjects and also comparing our controls to our
clinical cohort. Examples in the longitudinal processing stream tutorial have
only mentioned volu
Hi Nikhil,
If you are only interested in the norm.mgz you don't need the
longitudinal pipeline, because that is designed to give you more
reliable segmentations and surfaces.
Simply run 1 and 2 and you have the norm for all subjects / time points.
If you want to register them into the same s
Hi David,
in newer versions (not sure exactly when I added this) you can pass
-addtp to the -long run. That will add the time point to the study
without re-running the base. However this will probably introduce a
processing bias as this time point will be treated differently from the
other ti
Hi Yoon,
I usually run mri_glmfit directly and then look at the gamma map (that
is the average if you ran a one sample group mean analysis, which is
what you did, I think).
qdec is just a wrapper around glmfit so the file should be there, I am
not sure if qdec can visualize it directly? (am no
Hi Doug & Surfers,
I'm having this same issue. I'm running funcroi-table-sess on two
analyses (lh and rh). There was no 'log' folder in my working directory,
so I created it. Everythingran fine for the lh, but when I try to run
it in the rh I get
set: Variable name must begin with a letter
Dear Freesurfers,
Is there a way to visualize average absolute symmetrized percent
thickness/volume/area change (not significance map) using qdec or tksurfer or
other freesurfer tools?
I successfully generated correlation significance map using qdec for the
longitudinal data we processed, but I
Hi Katie, can you run it with -debug as the first arg and send me the
copious terminal output?
doug
On 08/30/2013 01:53 PM, Kathryn Devaney wrote:
> Hi Doug & Surfers,
>
> I'm having this same issue. I'm running funcroi-table-sess on two
> analyses (lh and rh). There was no 'log' folder in my
Thanks a lot!,Pablo
Date: Fri, 30 Aug 2013 11:38:26 -0400
From: fis...@nmr.mgh.harvard.edu
To: pablon...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
yes, any single file that is in the correct series should be fine
Bruce
On Fri,
Katica,
The file system in the physical computer is NTFS. But it looks like the
SUBJECTS_DIR is on a mounted filesystem. And your on a virtual machine.
Unfortunately there's lots of possibilities here for some type of
incompatibility with symbolic links.
Would it be possible for you to set the
Hi Pablo
yes, any single file that is in the correct series should be fine
Bruce
On Fri, 30
Aug 2013, pablo najt wrote:
Dear FS,
Following on my question about the initial format of my files for running
recon -all, I finally managed to get the Dicom files for our images.
However, as the imagi
Oh, I see. It must be the volume geometry being invalid. When I try it
with the new version of mri_surf2surf, the two surfaces are right on top
of each other.
doug
On 08/30/2013 09:22 AM, Franz Liem wrote:
> Hi again,
> just a clarification. The two surfaces in the image are single subject
>
Hi Pablo, each one of those files is a slice. Just pick one of them and
recon-all will find all the slices that also belong with that series
doug
On 08/30/2013 11:23 AM, pablo najt wrote:
> Dear FS,
> Following on my question about the initial format of my files for
> running recon -all, I fin
Hi Bruce this comes out from ls -ald $FREESURFER_HOME/subjects/fsaverage
drwxr-xr-x. 7 root root 4096 Oct 23 2012
/usr/local/freesurfer/subjects/fsaverage
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 2013 11:15 AM
To: Boric, Ka
I think this error
ln: failed to create symbolic link `./fsaverage': Operation not supported
is a problem with your file system. Are you using a FAT file system?
On 08/30/2013 11:41 AM, Boric, Katica A. wrote:
> Hi Bruce this comes out from ls -ald $FREESURFER_HOME/subjects/fsaverage
>
>
Hi Katica
does /usr/local/freesurfer/subjects/fsaverage exist? Do you have write
access to /mnt/hgfs/Linux_Share/subjects?
cheers
Bruce
On Fri, 30 Aug 2013, Boric, Katica A. wrote:
> Hi everyone!
> I am new to freesurfer, and I was processing and MRI using "recon-all
> -autorecon1 -autorecon
Hi Bruce!
Thanks for your fast response.
/usr/local/freesurfer/subjects/fsaverage does exists!
Thanks again,
Katica
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 2013 10:51 AM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.
Dear FS,Following on my question about the initial format of my files for
running recon -all, I finally managed to get the Dicom files for our images.
However, as the imaging protocol includes several modalities, (resting state,
functional, T1, DTI), we had to sort the dicom files. For my struct
Hi everyone!
I am new to freesurfer, and I was processing and MRI using "recon-all
-autorecon1 -autorecon2 -autorecon3" command and I have a message that the
processing was exited with ERRORS. When checking the recon-all. log it appears
that these are the error (highlighted in yellow):
#@# BA L
this:
drwxr-xr-x. 7 root root 4096 Oct 23 2012
/usr/local/freesurfer/subjects/fsaverage
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 2013 11:15 AM
To: Boric, Katica A.
Subject: Re: [Freesurfer] error in MRI processing
how abou
that probably means you don't have write access to the subject directory.
Can you run:
ls -ald /mnt/hgfs/Linux_Share/subjects
On Fri, 30 Aug 2013, Boric, Katica A.
wrote:
> It says:
> $ ln -s /usr/local/freesurfer/subjects/fsaverage
> ln: failed to create symbolic link `./fsaverage': Operation
It says:
$ ln -s /usr/local/freesurfer/subjects/fsaverage
ln: failed to create symbolic link `./fsaverage': Operation not supported
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nm
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, August 30, 2013 10:51 AM
To: Boric, Katica A.
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error in MRI processing
Hi Katica
does /usr/local/freesurfer/subjects/fsaverage exist
can you run:
cd /mnt/hgfs/Linux_Share/subjects
ln -s /usr/local/freesurfer/subjects/fsaverage
and tell us what it says?
Bruce
On Fri, 30 Aug 2013, Boric,
Katica A.
wrote:
> Hi Bruce!
> Thanks for your fast response.
> /usr/local/freesurfer/subjects/fsaverage does exists!
>
> Thanks again,
> K
Hi,
We figured out was the problem was. Just so others on the list are aware,
when deleting voxels from the brainmask.mgz or
brainmask.finalsurfs.manedit.mgz volumes in Freeview, you should verify
that the deleted voxels have a value of 1, not 0. The 5.3 version of
Freeview has a "Recon Edit
Hi again,
just a clarification. The two surfaces in the image are single subject surfaces
(the original lh.white and the transformed lh.white.ico6), not fsaverage6
surfs.
Best,
Franz
Am 30.08.2013 um 09:51 schrieb Franz Liem:
> Hi Doug,
>
> thanks a lot.
> I am using Darwin-snowleopard and c
Hi Doug,
thanks a lot.
I am using Darwin-snowleopard and centos6_x86_64.
What I am trying to do is to use the white surface as seed for probtrackx.
Therefore, I would like to reduce the number of vertices and at the same time
bring the surfaces into a common space (so that vertex x is meaning
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