Hello All,
I'm getting an error similar to another some months back.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09729.html
The command is failing on 2 of our subjects, but running properly for
others. For the 2 failed sessions, it's creating only the dof and Xtmp.mat
files in t
Albert,
It appears to be failing when the mris_compute_lgi script first attempts
a call to matlab. To debug, try this:
cd $SUBJECTS_DIR/dinghai_4/surf
mris_compute_lgi --i lh.pial --debug
and follow the output to trace where it is failing. notice that
mris_compute_lgi creates a temporary .m f
I assume that that flag (-washu_mprage) is somewhat antiquated, right?
That is, it was included for an older set of scans (generated at WashU
generated years ago before Siemens had its own MPRAGE sequence) that
happened to have darker gray matter, and doesn't need to be applied for
"modern" MPRAGE
Alex,
My code converts the FreeSurfer surfaces into caret format and applies the
appropriate transformations when Freesurfer is given data that is already in
Wash U standard space. It is based on things that Donna originally figured
out. Shortly, I will extend this to the volume parcellations ou
Alex,
The -washu_mprage flag affects mri_normalize and mri_segment. It
adjusts the parameters of those binaries to match the assumed intensity
profile in mprage scans, eg. to account for darker grey matter. I've
updated the help text in recon-all.
Nick
> As a side note, there appears to be a s
Yes,
I am currently giving freesurfer an atlas (711-2B / TRIO_Y_NDC to be
specific) transformed 111 MP-RAGE file. The concern is that if I use
mri_convert, I want to specifically return to the same 111 volume size
and space and I provided as accurately as possible (hopefully using
the inv
I am following up on some issues where we see some effects we really
don't expect when analyzing our data with qdec. They look like they
could be some slightly bad data from scan issues, segmentation problems,
etc. This is a large set of scans so I would like to script out a
routine to get the th
Alex,
We ran into the same problem a while ago for some of our studies. We
did the following:
1. Convert an Avi preprocessed T1 MPRAGE into a FreeSurfer-native
format and provided it the appropriate orientation and image center.
2. Next, we simply ran recon-all on this file (single MPRAGE). T
Hi all,
Just starting using Freesurfer, and while I did search the mailing
list archive, I didn't see a ready answer for this question:
I would like to use Freesurfer to generate surfaces for my subjects
(currently using Caret's SureFit routine), however I need to maintain
a specific atlas
mri_convert segmentation.mgz segmentation.nii
should do it
doug
Ed Gronenschild wrote:
> Hi,
>
> I would like to extract the WM and GM segmentations
> used for the final cortical thickness calculations as
> nifti files. How can I do that?
>
> Ed
>
> __
Can you send me your SUBJECTS_DIR, your command-line, and your working
directory in a way that I can cut-and-paste them into the shell?
doug
Victoria Williams wrote:
> Hi,
>
> I have successfully run 126 subjects through bbregister and
> mri_vol2vol in order to translate the wmparc volume into
you have to map the subject/surf/lh.thickness to fsaverage space as well
(again with mri_surf2surf).
doug
Feng-Xian Yan wrote:
>
>
> 2009/8/25 Feng-Xian Yan mailto:mimigi...@gmail.com>>
>
> Hi,
>
> First, I use mri_surf2surf (as follows) to map our subjects to
> fsaverage.
>
> mr
Hi,
I have successfully run 126 subjects through bbregister and mri_vol2vol in
order to translate the wmparc volume into TBSS space. However, there are 2
subjects that exited prematurely from bbregister. I think it may have to
do with my naming system? 126 of the subjects have the subjid
CVRA
Hi,
I would like to extract the WM and GM segmentations
used for the final cortical thickness calculations as
nifti files. How can I do that?
Ed
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinf
Hi Fatima --
Ahmed, F, Me wrote:
> cd /usr/local
> tar xzvf freesurfer-Linux---full.tar.gz
>
>
> and I got the following error:
>
> tar: freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar: Cannot
>
>>> open: No such file or directory
That error in fact does make sense. The 'tar' command is
Hi Nick,
You probably don't recall but you were trying to help me sort out a few
problems with my FS a while back. You told me to uninstall and then reinstall
to hopefully see if the problem fixes itself. The problems I face now are with
the installation, I followed the commands on the wiki sit
16 matches
Mail list logo
