Hi Mahmoud
were you able to create a symlink to fsaverage in your SUBJECTS_DIR? If
not, that is the reason for this error
Bruce
On Thu, 18 Sep 2014, Mahmoud wrote:
Dear all,
After running "recon-all -i $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
-subject case018_tp2 -all" I'm always getting
Dear all,
I am running FreeSurfer version [recon-all,v 1.313.2.6 2010/08/04] on an
Ubuntu machine.
After updating my system from Ubuntu 12.04 to Ubuntu 14.04 I get a
segmentation fault when I try to resample images using mri_convert:
/mri_convert -vs 1 1 1 /folder/original_image.nii.gz /folde
There is no direct way. But you can try this workaround:
Write all the screenshot command in a text file, line by line like this:
-v brain.nii
-viewport sagittal -slice 80 127 127 -ss sag1 -noquit
-viewport sagittal -slice 127 127 127 -ss sag2 -noquit
…
Then run this command:
freeview -cmd cmd
Hi Bruce,
Actually I couldn't. It says: ls: cannot access
/usr/local/freesurfer/subjects/fsaverage: Too many levels of symbolic links
And even I couldn't cd to fsaverage !
In fact there is no directory under SUBJETCS_DIR named fsaverage, it seems
the fsaverage under SUBJETCS_DIR is just a broken
can you tell us what your FREESURFER_HOME is and what your SUBJECTS_DIR is?
You will need to remove the broken link probably
On Fri, 19 Sep 2014, Mahmoud wrote:
Hi Bruce,
Actually I couldn't. It says: ls: cannot access
/usr/local/freesurfer/subjects/fsaverage: Too many levels of symbolic link
Bruce,
Here is the info when I open a new terminal:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_
the directory /usr/local/freesurfer/subjects is for subjects that we
distribute and NOT where you should be putting your subject data. Is that
what you are doing? You may have overwritten the fsaverage dir there. Can
you run:
ls -l /usr/local/freesurfer/subjects/fsaverage
and send us the res
Bruce,
I already had my data in a shared folder (/mnt/hgfs/mydata) but I got the
permission error the same point that I got the symlink error lastly. So, I
tought that might be due to something related to shared directory.
Then I copied my subjects under the $SUBJECTS_DIR but got the symlink error
Hi all
I was wondering whether it’s possible to get the talairach coordinates
associated with each label in the segmentation. I would like to use
Freesurfer’s segmentation for analysis in Matlab.How to create a text file
with the talairach coordinates of each label (or of a specific label, by
yes, you symlinked it to itself which is why you are getting the infinite
recursion error. You need to delete
/usr/local/freesurfer/subjects/fsaverage
and download the fsaverage dir again, put it in that directory, then
symlink from your /mnt/hgfs/mydata/fsaverage to
/usr/local/freesurfer/sub
Bruce,
Thank you for your follow up and advice. Please let me know:
1- How to download the fsaverage again?
2- should I do the symlink manually or it will be done by recon-all later ?
3- What steps should I take before running the recon-all -all ? should I
create any specific directory? set any pe
Dear Freesurfer's experts,
I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing
pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.
The first step has to be the correction of gradient-nonlinearity-induced
distortion. The correction is then done with a
Hi,
I have a question about spherical registration, and I couldn't find a
relevant answer in the mailing list.
I have two subjects S1 and S2 with corresponding functionals. I want to
show the functionals of each subject on the surfaces of the third subject
S3. I have .sphere files for S1, S2, and
Hi,
I suggest you start with the documentation that accompanies the recently released HCP pipelines.
see
http://www.humanconnectome.org/documentation/HCP-pipelines/
and the link therein to the pipelines on GitHub.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Hello Alessandra,
This is a known issue with pre-freesurfer v5.3 releases and the most
recent version of Ubuntu. To fix the issue, if you have access to a
machine that still runs Ubuntu 12.04, please do the following:
1) On the Ubuntu 12.04 system, find the find the file "libcrypt-2.*.so"
usual
Thank you Michael for this link !
However, it seems that we have to install very precise versions of FSL and
Freesurfer.
Once we get *fsl-5.0.6* package (
http://fsl.fmrib.ox.ac.uk/fsldownloads/oldversions/), how to install this
one and which wiki to follow ?
Cheers,
---
More precisely how to install *fsl-5.0.6* on ubuntu 12.10 or 14.04 ?
Thanks !
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
2014-09-19 17:18 GMT+02:00 Matthieu Vanhoutte :
> Thank you Mi
The pipelines documentation should include fairly extensive documentation to get you going.
If you have further questions, you should switch over to using the HCP-Users list.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center f
Bruce,
By "symlink from your /mnt/hgfs/mydata/fsaverage to
/usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
/mnt/hgfs/mydata/fsaverage /usr/local/freesurfer/subjects/fsaverage" ?
which fsaverage is the target ?
Thanks,
Mahmoud
On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud wrote:
> Bruce,
the easiest thing to do is:
cd /mnt/hgfs/mydata
ln -s /usr/local/freesurfer/subjects/fsaverage
then you don't have to worry about source and target. It will implicitly
create the symlink in $PWD
cheers
Bruce
On Fri, 19 Sep
2014, Mahmoud
wrote:
Bruce,
By "symlink from your /mnt/hgfs/my
> Bruce,
>
> By "symlink from your /mnt/hgfs/mydata/fsaverage to
> /usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
> /mnt/hgfs/mydata/fsaverage /usr/local/freesurfer/subjects/fsaverage" ?
> which fsaverage is the target ?
>
> Thanks,
> Mahmoud
>
The "target" fsaverage is the one that ca
Here is the proper link.
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/fsaverage.tar.gz
>> Bruce,
>>
>> By "symlink from your /mnt/hgfs/mydata/fsaverage to
>> /usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
>> /mnt/hgfs/mydata/fsaverage /usr/local/
Bruce and Zeke,
Thank you so much for your advice.
The last question before running the recon again. if I say:
cd /mnt/hgfs/mydata
ln -s /usr/local/freesurfer/subjects/fsaverage
It means that I shouldn't already have the fsaverage under /mydata
directory, right ?
Mahmoud
On Fri, Sep 19, 2014 a
yes, that is true. If it's already there the symlink will fail. You
should be able to rm it if it is there an incorrect (or leave it if it is
there and correct)
On Fri, 19 Sep 2014, Mahmoud wrote:
Bruce and Zeke,
Thank you so much for your advice.
The last question before running the recon aga
Mahmoud,
If I recall correctly, your on a virtual machine with the /mnt/hgfs/mydata
directory being a shared directory, and you werent able to write to it
when running recon-all.
So, what you want to do is create another directory within your virtual
machine that holds your subjects data. You wil
Zeke,
I created another directory named "volumetric" and put my data under it.
To final check before running the recon-all, here is the info from terminal:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME
I believe if you simply run:
$> recon-all -i /volumetric/Case018/case018_tp2/22-1.dcm -subject
case018_tp2 -all
You should be all set. You do not need to type any of the following commands:
> clear
> cd /volumetric
> ln -s /usr/local/freesurfer/subjects/fsaverage
-Zeke
> Zeke,
>
> I create
Hi,
To convert GIFTI files to the Freesurfer files, I just need to do
something like this?
mris_convert F99.R.inflated.74k_f99.surf.gii rh.inflated
Thanks,
Reza
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu
Dear all,
Is there a way to get a count of the voxels in a manually drawn ROI while
retaining each voxel's intensity value? *In particular, I would like to
get a count of how many voxels in this manually drawn ROI fall above and
below an assigned intensity threshold.*
I have used mri_segstats to
Hi Karishma
if you draw an ROI and save it in label format you can use mri_label_vals
to generate a text file with the value of every voxel in the label. That
can then be imported into matlab to do whatever you want.
cheers
Bruce
On Fri, 19 Sep 2014, Karishma Smart wrote:
Dear all,
Is the
Indeed I ran mri_glmfit-sim. What file is the output of mri_segstat?
The cache.th13.abs.sig.ocn.annot contains the significant clusters it that
correct? So to get individual mean values from cluster 1 for example where
should I look?
Thanks!
Celine
>
> Have you run mri_glmfit-sim? It will create
should be something like cache.th13.abs.y.ocn.dat
also, you can look in mri_glmfit-sim --help to get info about each
output file
On 09/19/2014 04:47 PM, Celine Louapre wrote:
> Indeed I ran mri_glmfit-sim. What file is the output of mri_segstat?
> The cache.th13.abs.sig.ocn.annot contains the
You can use mri_label2label specifying your subject as the source and
fsaverage as the target and --regmethod volume. This will convert the
coordinates to mni305 space. You can then use read_label.m to load the
label into matlab
On 09/19/2014 09:32 AM, ri wrote:
> Hi all
> I was wondering whet
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