Hey all,
I'm getting the following message while using qdec
Error in Analyze: command failed: mri_glmfit --y
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/y.mgh --fsgd
/Users/Preissler/Desktop/Julia_FreeSurfer/korrigiert/qdec/Untitled/qdec.fsgd
dods --glmdir
/Users/Preis
>From my understanding qdec fits a glm to each vertex. It also smooths the
data.
>From the documentation I do not have a clear understanding of whether qdec
uses smoothed data for input (It appears that is does) or smooths the
coefficients or t-tests after analysis, or both.
Additionally, the res
Hello,
I've been running Freesurfer v4.0.2 in Debian and now wanted to use a
computer that has Red Hat 9 to also run some subjects. Could you let me
know if it's possible to download version 4.0.2 for Red Hat?
Many thanks,
Lucia
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Hi there,
After I install the latest version of freesurfer on my Linux machine,
I got the following errors:
tar: freesurfer/diffusion/mgh-dti-seqpack: Cannot utime: Operation not permitted
tar: freesurfer/diffusion: Cannot utime: Operation not permitted
tar: freesurfer: Cannot utime: Operation no
Richard,
Just the input data is smoothed (during the recon-all -qcache stage run
outside of qdec).
The patches that appear in a results display are not 'patches' in any
explicit sense, but just what is displayed due to the default thresholds
that qdec uses. You can adjust those thresholds via th
Lucia,
You can get a copy of it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/rh9
Nick
On Mon, 2008-12-08 at 15:32 +, Lúcia Garrido wrote:
> Hello,
>
> I've been running Freesurfer v4.0.2 in Debian and now wanted to use a
> computer that has Red Hat 9 to also
Bai Xue,
Try this:
gunzip -c freesurfer-Linux...(your download filename) | tar xvf -
(where the -c arg is the name of your freesurfer tarball).
Nick
On Mon, 2008-12-08 at 10:34 -0500, Bai Xue wrote:
> Hi there,
>
> After I install the latest version of freesurfer on my Linux machine,
> I g
Julia,
Does it give any further details in the error message? It would be in
the terminal output (the popup box would not have the full message). Do
all of those files in the command line exist and are readable?
You can also try copy-and-pasting that command directly to the terminal
(outside of
Try adding --noreshape to both mri_vol2surf and mri_surf2surf cmd lines.
doug
Alexandru Hanganu wrote:
Dear Freesurfer users,
We have an MNI mask and we want to apply this mask on a group of
subjects for small volume correction.
so we did the following steps:
1. cd $SUBJECTS_DIR/fsaverage/
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
I would probably use --ocn with mri_volcluster to create a single volume
in which each voxel value is the cluster number it belongs to. Then
split them out like:
mri_binarize --i ocn.mgh --match 1 --o cluster-0001.mgh
doug
Gregory Dierksen wrote:
Hi,
I'm trying to use the mri_volcluster c
Thank you Nick, and Doug for your answers. I used both "--reshape" flag and
"--noreshape" flag and the results after "mri_segstats" were in both cases:
.
.
.
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 2 segmentations
Computing statistics for each
Hi, Nick
I tried, but still has the same error.
Thanks.
Bai
On Mon, Dec 8, 2008 at 11:36 AM, Nick Schmansky
<[EMAIL PROTECTED]> wrote:
> Bai Xue,
>
> Try this:
>
> gunzip -c freesurfer-Linux...(your download filename) | tar xvf -
>
> (where the -c arg is the name of your freesurfer tarball).
>
>
Bai Xue,
Does freesurfer untar itself anyway? In other words, does it untar
fully, but just will those error messages? It sound like it if the
testing you tried (from our example tests) worked ok. You can ignore
the utime message for the mgh-dti-seqpack file for now I think. That
util is not p
what's your cmd? You need to make sure to add --in lh.thickness to get
thickness in the summary file
Alexandru Hanganu wrote:
Thank you Nick, and Doug for your answers. I used both "--reshape"
flag and "--noreshape" flag and the results after "mri_segstats" were
in both cases:
.
.
Yes, I think untarring freesurfer is fine. Will this be a problem if I
process dti in the future?
Thanks.
Bai
On Mon, Dec 8, 2008 at 1:38 PM, Nick Schmansky
<[EMAIL PROTECTED]> wrote:
> Bai Xue,
>
> Does freesurfer untar itself anyway? In other words, does it untar
> fully, but just will those e
Hi Freesurfers,
I am a little stuck. I have some 3T data that has had the skull stripping
manually corrected. In addition we have some unusual bias artifacts that FAST
seems to handle better than n3, so I have done my own bias correction. Since I
had to run FAST anyway, I created brainmask.m
Hi
I need one piece of info that I can't seem to find anywhere (after 1h
of searching).
What exactly do the numbers in register.dat correspond to (I know for
the first four rows, but the last four rows are still a "mystery")?
Can I manually temper with that info (if I know I translated an image
Julien,
This posting by Patrick Schikowski might help:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08085.html
Nick
On Mon, 2008-12-08 at 19:12 -0800, Julien Dubois wrote:
> Hi
>
> I need one piece of info that I can't seem to find anywhere (after 1h
> of searching).
>
> Wha
Hi, Mr. and Mrs
I want Tutorial file of fsfast.
But I didin't get it from the following pass.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsfast-tutorial/fsfast-tutorial.subjects.tar.gz
If you know about that please let me know.
Thank you for your help.
Best regards,
Kenta
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