How many files are in the dicom folder? Try copying one of them to a
different folder and running it on that one file (it will only be a
test, the output file will not be correct)
On 9/9/14 1:12 PM, Nooshin Zadeh wrote:
Yes. It just hang there. I even let it run for few days! and no outco
Yes, you can just run
/path/to/your/local/copy/mri_glmfit-sim
On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
> Hi Doug,
>
> I don't seem to have the permission to change the contents of that folder. So
> I can't really copy it over. Is it possible to run this locally? I'm working
> o
We have extended the Alzheimer's Disease Sage/DREAM Challenge #1 submission
period to October 17th -- Time to enter!
https://www.synapse.org/#!Synapse:syn2290704
Of particular interest to the members of this mailing list is subchallenge
3, which leverages brain imaging
(
FreeSurfer was used in
Hi Doug,
I don't seem to have the permission to change the contents of that folder. So I
can't really copy it over. Is it possible to run this locally? I'm working on a
linux workstation at Martinos and when I ask the source, it gives me that
folder:
>>which mri_glmfit-sim
/usr/local/freesur
You can just copy it over the old one (but make a backup of it first)
On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
> Hi Doug,
>
> Thanks for your reply. I can certainly test it. Could you tell me how I can
> run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' that
Hi Doug,
Thanks for your reply. I can certainly test it. Could you tell me how I can run
this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' that I use
is under '/usr/local/freesurfer/stable5_0_0/bin/'
Best,
Hamdi
From: freesurfer-bou
Yes. It just hang there. I even let it run for few days! and no outcome.
On Sep 9, 2014 12:19 PM, "Bruce Fischl" wrote:
> Hi Nooshin
>
> does it just hang there? How long do you let it run?
> Bruce
> On Tue, 9 Sep 2014, Nooshin Zadeh wrote:
>
> Dear FreeSurfer experts,
>>
>> I get a new message
Hi guys!
We would like to install the latest and greatest FreeSurfer on the processing
cluster used by the CNDA at Washington University. We're thinking about
installing the 5.3.0-HCP, and then over that, the released 5.3.0 patches.
We're looking for verification that doing the install this w
Hi Neeraj - The libnetcdf error you're getting probably means that
you should install a different build of freesurfer (centos 4 instead
of centos 6). Which one are you currently using?
In the future please email the freesurfer list instead of me personally
with questions about tracula. The p
Hi Robby - Since you're running it locally and not on a cluster, you can
just run bedpostx directly:
bedpostx /media/mri/DATAPART11/ROBBY/FREESURFER/T1/INP_080_LISA_V_1/dmri
a.y
On Tue, 9 Sep 2014, Robby De Pauw wrote:
>
> Dear Anastasia, Barbara & FS-community,
>
> The preprocessing step of
Hi Nooshin
does it just hang there? How long do you let it run?
Bruce
On Tue, 9 Sep 2014,
Nooshin Zadeh wrote:
Dear FreeSurfer experts,
I get a new message when I use "mri_convert" command to convert dicom to mgz. I
used to apply this command before and there was
no problem. I wonder what i
Can you please attach the trac-all.log file, which has the entire output
from beginning to end? Ofter something goes wrong earlier that causes the
program to fail later in the process.
Also, we'll need your original configuration file. Thanks!
On Mon, 8 Sep 2014, Katherine Damme wrote:
Hel
That means that you need to add something like
--surface fsaverage lh
the above assumes that you used the left hemi of fsaverage
On 09/05/2014 02:56 AM, Minjeong Wang wrote:
>
> Dear all,
>
> i have some problem with mri_glmfit.
>
> The error message is "you must use '--surface subject hemi'
Why do you have your activation in a .w file? If you can save it as
.mgh, then things get a lot easier. You can convert it to mgh using
mri_surf2surf. You'll need to convert the thickness to mgh with
mri_convert lh.thickness lh.thickness.mgh. Then load the two mgh files
into matlab, eg,
thick
This is tough to interpret, but basically, yes it would be
0-.004mm2/year. It is not quite right to say that it is at that vertex
because of smoothing, but in that area. It is also hard to say what the
total change would be for a cluster. One could sum the changes over the
cluster vertices, bu
On 09/06/2014 07:10 AM, Reza Rajimehr wrote:
> Hi,
>
> I have a basic question, but the answer can be useful for others as well.
>
> I am doing a customized preprocessing of monkey functional data in FS-FAST
> v5.3. After motion correction and before functional-anatomical
> registration, I want to
the commands I gave you will do this
On 09/06/2014 07:47 AM, Reza Rajimehr wrote:
> I forgot to mention that I want to use undistorted EPI volumes for the
> functional-anatomical registration.
>
>
>> Hi,
>>
>> I have a basic question, but the answer can be useful for others as well.
>>
>> I am doin
Dear FreeSurfer experts,
I get a new message when I use "mri_convert" command to convert dicom to
mgz. I used to apply this command before and there was no problem. I wonder
what is the reason that I get the new message. In addition, it does not
create mgz file, and goes to infinite loop.
*mri_c
Hi Markus,
Thank you for this, yes I am running Mac OS 10.9.2, and the freesurfer
command freeview loads the data fine when I start up matlab from the bash
terminal (even without using XQuartz, my equivalent of X11) and call this
command.
Thanks for the quick help!
Barbara
On Tue, Sep 9, 2014 a
Hi Gayane,
what happens if you run the mris_calc command directly? Also check if
all the inputs really exist. It could be that you need to update
mris_calc there was a problem with long file names in an earlier
version. Which FS version are you using?
Best, Martin
On 09/09/2014 09:51 AM, Ga
Dear list,
I'm running longitudinal two stage model as is described in the tutorial
here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel
First, I've proceeded with longitudinal pipeline all my data, second, I've
created longitudinal qdec table, and then, I've started to qcache my data,
wh
Dear Anastasia, Barbara & FS-community,
The preprocessing step of Tracula was succesfully completed. However
when I try to do the next step: fitting the Ball & Stick model I get
another error:
mri@ge24c165:/media/mri/DATAPART11/ROBBY/FREESURFER$ trac-all -bedp -c
dmrirc.info
INFO: SUBJECTS
Hi Anastasia,
Thanks for taking a look and point that out. I'll have to be more careful
in checking the source images, instead of going by the notes (and memory of
events years past) left by the previous engineers on the project.;)
-Peggy
On Mon, Sep 8, 2014 at 6:21 PM, Anastasia Yendiki <
ayend
Hi Andrea
what is the background image? This is usually either a failure of the
intensity normalization or of the surface deformation/segmentation to
adaptively estimate the underlying intensity distributions of the
gray/white matter. If you look in recon-all.log for that subject you will
fin
Hi Joann
it looks like some white matter is not being identified in the ?h.white
surface. You need to diagnose why this is happening. It's probably an
inaccurately corrected topological defect. Have you gone through the
tutorials? You will likely need to add some wm voxels back in. If you
uplo
Hi Barbara,
You haven't told us which OS you use.
For example in Mac OS it is necessary to start up MATLAB by typing matlab
into the X11 terminal, otherwise the system OS will not recognize the
commands given via matlab (e.g. system('mycommand') .)
Best,
Markus
2014-09-09 13:45 GMT+02:00 Barbara
Dear Freesurfers,
Is there a way of calling freesurfer-scripts from within MATLAB?
I know there are some setups needed to make MATLAB understand where it can
find the commands (I have done this before with FSL).
I am using bash, and when I type the Freesurfer commands in a terminal by
hand, they w
mris_expand may do what you want.
You can use it to shrink or expand the points on a surface by a fixed
percentage or a fixed distance.
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
From: freesurfer-boun
Dear Freesurfers,
After running recon-all, the wm surfaces are too close to the pial surface,
some gray matter is segmented as white matter as seen in the attached
picture (red cross: a bigger cortical part is included in the white matter).
How can I shrink the wm surface?
Thank you for your he
Hi Will,
Just to clarify, what version of FS are you using? I think it might not be
5.0 and I don't know if everything aplies if we are using different
versions.
1) Yes, it is only based on the pial surface (and these command lines are
for the aparc, DK altas). The second set provides the surfac
Ok Eugenio,
I just have a final consideration.
Whenever this last step will be implemented, there will still will be the
problem of how to binarize those subfields in a way that makes sense.
Plese correct me if I'm wrong: given that at the end counting all the
non-zero voxels will always overesti
Hi again, Luigi,
this sentence that you wrote summarizes everything pretty well:
"I think that the posterior files outputted by freesurfer are missing the final
step of required to each voxel to the single label with the highest posterior
prob."
We will implement this in the next FS release.
Re
Dear Eugenio,
/"assign to each voxel the label with the highest posterior probability"
/implies that each voxel must belong to *one and only one* label, right?
I've found that this is not the case with the posterior_*.mgz files
outputted by freesurfer, where each voxel (especially the ones wi
Thanks Andreia, this does appear to have worked. Please forgive my
ignorance but I do just want to double check two things;
1) The first commands you have given provide the stats for the two
hemispheres of the cerebral cortex only based on the pial surface, whereas
the second set of commands provi
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