Dear Priti
The bedpostx works fine on the data if I run it outside of tracula.
The command /home/kutato12/freesurfer/bin/fsl_sub_seychelles -T 60 -m a -N
bedpostx_pre -l
/home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs
${FSLDIR}/bin/bedpostx_preproc.sh
Hi Doug,
Thanks for your help! No, the current directory is the Project directory
(refering to naming conventions in
http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct). It is
identical to $FUNCTIONALS_DIR.
The rtopy.self.lh folder is in the Sess0x directory and contains only
yes, B is correct. The error says that it cannot find matlab. Is it in
your path?
doug
On 5/25/12 9:16 AM, Michael Bannert wrote:
Hi Doug,
Thanks for your help! No, the current directory is the Project
directory (refering to naming conventions in
If the source is an annot, then you need to use --sval-annot Is this
causing a problem?
doug
On 5/24/12 6:48 PM, Arno Klein wrote:
hello!
in mri_surf2surf, does anyone know how to specify the source and
target formats if --sval is annot without using --sval-annot, as in
--sfmt or --tfmt?
hi doug,
we are trying to figure out if for annot we *have to* use sval-annot or if
there is a way to do it with sval?
cheers,
satra
On Fri, May 25, 2012 at 9:46 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
If the source is an annot, then you need to use --sval-annot Is this
causing
Hi Doug,
Yes, that was the problem. I think Freesurfer expects that you start Matlab by
typing matlab in the terminal (as opposed to matlab2010a which is what I
usually do). So I created a new symbolic that takes care of that.
Now I got the error message ERROR: TR mismatch between analysis and
This is going to be updated in the next version of freesurfer. There have
been some compatibility issues with the latest version of bedpostx that
we've had to fix. For now please run bedpostx by itself. Thanks!
On Fri, 25 May 2012, Gabor Perlaki wrote:
Dear Priti
The bedpostx works fine
Currently, yes. If this is a burden for you, I could hack something.
There might be other ways such as converting the annot into a
segmentation (mris_annotation2label), passing that to surf2surf with
--sval (and --mapmethod nnf), then converting the output back to an
annotation
hi doug,
thanks. we just wanted to verify that annot's are special. no need to hack
anything!
cheers,
satra
On Fri, May 25, 2012 at 11:27 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Currently, yes. If this is a burden for you, I could hack something.
There might be other ways such
Hi Leon,
if I recall correctly the wm surface is looking at intensity gradients in the
brain.finalsurfs.mgz (I think). So please have a look at that file and see
whether you have some weird issues in that file. The orig surface is created
from the wm.mgz and so will reflect edit you made
Hi Rashimi,
no idea what is causing this, as you say the scripts look OK. Have you
tried re-running the longitudinal run from scratch, to make sure this is
not caused by earlier data or by some I/O problem?
Best, Martin
On Fri, 2012-05-25 at 16:41 +, Rashmi Singh wrote:
Thanks Martin,
I
Dear experts,
I'm an MSc student and part of my final project is related to the
measurement of the volume of the hippocampus. The last thing I have to do
is to compare two softwares, FSL and Freesurfer.
On Freesurfer, I've used the following commands:
recon-all -i where_my_subject_is
Hi, Sebastian and Bruce
I think I have found the reason: there are low intensity values at the
precentral region (~1) that are almost invisible when viewed using the gray
color scheme in FS. When I converted the wm.mgz to nifti format and viewed it
in FSL using red-yellow color scheme. They are
Hi Leon
you can either change the windowing in tkmedit, or load the wm.mgz as an
overlay of segmentation in either tkmedit or freeview.
cheers
Bruce
On Fri, 25 May 2012,
Leon wrote:
Hi, Sebastian and Bruce
I think I have found the reason: there are low intensity values at the
precentral
Hello,
I am trying to run make_average_subject on my data using the --xform
talairach.m3z option, but make_average_volume fails because I get an error
during mri_vol2vol:
ERROR: transforms/talairach.m3z does not start as 'MNI Transform File'
Any suggestions? I can make an average subject
Hi Kushal, can you try this version of vol2surf?
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux
If that still fails, please tar up the subject and functional and upload
it to our file drop system at the end of this email.
doug
On 05/25/2012 04:03 PM, Kushal
doug,
thanks dougbefore i do thati have two questions which may take care of
mri_vol2surf issues
1- mri_vol2surf command needs to specify register.dat file
i have been using register.dat file for vol2surf from reg-feat2anat
output.is that the register.dat file i am
On 05/25/2012 04:30 PM, Kushal Kapse wrote:
doug,
thanks dougbefore i do thati have two questions which may take care
of mri_vol2surf issues
1- mri_vol2surf command needs to specify register.dat file
i have been using register.dat file for vol2surf from reg-feat2anat
@doug
no doug...this orig.mgzerror was before segmentation fault error started
showing up.hence i wanna see if why it gave that lemme take a look and
will keep u updated
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Kushal Kapse
Hi, Sebastian
Thank you very much for your information. It is very helpful.
Yes, my intention is to build a surface template based on my subjects for
surface-based analyses. As i am fairly new to FreeSurfer, here is my original
plan and correct me if I am not heading to the correct direction:
i was talking about this issue
mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi
lh --projfrac 0.5 --out lhfunc.nii.gz
srcvol = func.nii.gz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
The register.dat file is a text file. The first line has the name of the
subject. It looks like the subject name was
15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls
If either of those are not correct, then it will not determine the path
correctly.
Does that orig.mgz
Sorry, I just noticed that your command line is wrong. But that is not the one
that is seg faulting. The one that seg faults is the correct command
doug
On 05/25/2012 04:56 PM, Kushal Kapse wrote:
orig.mgz file is on 15446_03908/mri/orig.mgz
yes the subject name and the directory path is
well...
it seems the seg fault occured due to i was using a 4D func file and not
3ddoes the vol2surf does only on 3d func data ?how would i do that for
4D time series?
please let me know
thanks
kk
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Kushal
it works for 4D, we do it all the time. Is the registration good? Did
you check it visually with tkregister2? You can visualize it with
tkregister2 --mov func.nii.gz --reg register.dat --surfs
doug
On 05/25/2012 05:45 PM, Kushal Kapse wrote:
well...
it seems the seg fault occured due to i
yes ..the registration is nicely aligned and i did check the green-lines
alignment in tkregister2
is their any other reason for it showing segmentation fault
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Kushal Kapse kka...@mail.med.upenn.edu
Cc:
Not that I can think of. Did you try that new version?
On 05/25/2012 05:58 PM, Kushal Kapse wrote:
yes ..the registration is nicely aligned and i did check the green-lines
alignment in tkregister2
is their any other reason for it showing segmentation fault
- Original Message -
Hi Ana,
if this is on a single subject, anything can happen.
Also you can run that in a single step:
recon-all -i ... -autorecon1 -autorecon2 -s output_name
Best, Martin
On Fri, 2012-05-25 at 18:48 +0100, Ana Arruda wrote:
Dear experts,
I'm an MSc student and part of my final project is
doug,
did try new version..it worked fine...but seems tht new version doesnt support
.w as output format; like in the tutorial online.what output format does
the new version vol2surf likes?
thanks
kk
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Kushal
I don't think it ever supported w files ... you can use mgh /mgz format.
It will also produce nifti files, but they might not always be legal
nifti files. FreeSurfer will always be able to work with them, but other
software packages might not.
doug
On 5/25/12 8:19 PM, Kushal Kapse wrote:
i tried .nii.gz and they didnt work.i will try .mgz file and keep u
updated,...
thanks
kk
- Original Message -
From: Douglas Greve gr...@nmr.mgh.harvard.edu
To: Kushal Kapse kka...@mail.med.upenn.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 25, 2012 8:23:47 PM
Subject:
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