Because there is no response, I sent it again.
I just checked the problem and guessed there is something wrong in the
default setup. Is it corrected? what information do you want?
Xiaochu Zhang PhD
Visiting Research Fellow
Neuroimaging Research Branch
National Institute on Drug Abuse - IRP
If you have the Nvidia graphics driver, you probably need to update it.
As root, run 'nvidia-installer --update'.
On Fri, 2008-12-05 at 10:47 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:
> Because there is no response, I sent it again.
>
> I just checked the problem and guessed there is somethin
Hello,
I am a new freesurfer user. I have been trying to run recon-all on our data
and have been unable to do so because recon-all crashes everytime at the
same spot.
Here is the error I get when I run recon-all with autorecon1 or when I run
it with -nuintensitycor
*Iteration 1 Fri Dec 5 12:03:1
Sid,
1) when recon-all is finished on a subject, there are a number of stats
found in the /stats directory. for the additional ones you want,
you can use mris_anatomical_stats. see 'mris_anatomical_stats --help'.
ex. mris_anatomical_stats -a aparc -t lgi subjid lh
see also 'aparcstats2table' to
Dev,
What happens when you type:
nu_estimate_np_and_em
you should see:
nu_estimate_np_and_em, version 1.10
Usage: nu_estimate_np_and_em [-help] [options] input_volume.mnc
nu_field.imp
Incorrect number of arguments
do you have perl installed at /usr/bin/perl ?
do you have another installati
Jake,
Nothing has changed in stable3. It was retired as a code base when
stable4 was released. That "ispl failed" problem is something outside
of freesurfer.
Nick
On Thu, 2008-12-04 at 14:33 -0500, [EMAIL PROTECTED] wrote:
> Hello!
>
> I was just wondering if there is anything going on with
Nick,
When I type nu_estimate_np_and_em, I did indeed see the message you
mentioned. I also checked and found perl at /usr/bin/.
I didn't find any other installations of the mni tools in my path.
Are these the only things that usually cause recon-all to fail like this?
Any other ideas why it is fa
what OS are you using? what version of perl does it have? what is the
output of:
env | grep MNI
On Fri, 2008-12-05 at 13:51 -0600, Devdutta W wrote:
> Nick,
> When I type nu_estimate_np_and_em, I did indeed see the message you
> mentioned. I also checked and found perl at /usr/bin/.
> I didn'
This is the output of env | grep MNI:
MNI_PERL5LIB=/usr/local/imsw/freesurfer/mni/lib/perl5/5.8.5
MNI_DIR=/usr/local/imsw/freesurfer/mni
MNI_DATAPATH=/usr/local/imsw/freesurfer/mni/data
I am using Red Hat Enterprise Linux 5
Dev
On Fri, Dec 5, 2008 at 1:57 PM, Nick Schmansky <[EMAIL PROTECTED]>w
Hi Nick,
Thank you so much for your help!
Recently, I tested it strictly following your instruction. However, I
met a problem in the last step "mri_segstats ". They gave me the error
information: "ERROR: dimension mismatch between input volume and seg".
I checked the old mails in the list. Some one
Hi,
I'm trying to use the mri_volcluster command to make label files from a
single volume of binary voxel clusters. Once I have split the volume into
individual label files I want to convter the label files back into
individual cluster volumes (I am trying to use mri_label2vol to do this).
T
Zhang,
You could perform the steps you show in 1., where you sample your ROI
directly to the subjects surface, rather than going through the
fsaverage subject. Ultimately, you would (or should) end-up with the
same result as that from following the steps in the wiki page (going
through fsaverage)
Hi,
when running qdec the following error shows up. It is possible to run the
analysis for the lh. thickness and area but not for the same in rh.
In the single subject folders the averages for rh. are missing. qcache did run
without any error messages.
I thought it could have something to do wit
it means that subject is inconsistent. Try running
recon-all -s 4964-14_recon -hemi lh -make all
cheers
Bruce
On
Fri, 5 Dec 2008, Julia Altenburg wrote:
Hi,
when running qdec the following error shows up. It is possible to run the
analysis for the lh. thickness and area but not for the sa
Julia,
Most likely the processed data for that subject is out of sync (stuff
rerun later and out of order). If you run:
recon-all -s subjid -make all
then it should do nothing if all the data files were created in the
right order. I would add -dontrun to that recon-all command so it just
print
I just checked the demension information and found they are not same.
Do you think which one is wrong?
Thanks a lot!
Volume information for lh.thickness.fsaverage.mgh
type: MGH
dimensions: 163842 x 1 x 1
voxel sizes: 1., 1., 1.
type: FLOAT (3)
fov:
Xiaochu,
The dimensions for lh.thickness.fsaverage.mgh are correct, the ones for
lh.fsaverage.ROI5.mgh are not. They should be the same (163842x1x1).
Did you create lh.fsaverage.ROI5.mgh like this:
cd $SUBJECTS_DIR/fsaverage/surf
mri_vol2surf \
--mov /path/to/ROI5.nii \
--reg TT_avg152T1_to_
Thank you very much! However, I just checked it and I used ATI graphic
card but not NVIDIA card. What information do you think is benefit to
clear the problem? I will send to you.
Thanks a lot!
Xiaochu Zhang PhD
Visiting Research Fellow
Neuroimaging Research Branch
National Institute on Drug
I RUN:
[EMAIL PROTECTED]:/data2/379/ASL/temp/fsaverage/surf> mri_vol2surf --mov
../../ROI5.nii --reg TT_avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1
--interp nearest --hemi lh --out lh.fsaverage.ROI5.mgh
THE OUTPUT:
srcvol = ../../ROI5.nii
srcreg = TT_avg152T1_to_fsaverage.dat
srcregold = 0
s
Xiaochu,
My bad, I see the problem now. I was using our 'dev' enviro, which
doesnt 'reshape' the data (never mind that detail) whereas
'stable' (public) does.
So, just add --reshape to the end of the mri_surf2surf command, as the
updated instruction here show:
https://surfer.nmr.mgh.harvard.edu
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