Dear optseq2 developers,
I would like to use optseq2 to develop optimal sequence for my MRI experiment.
I have a windows machine (Windows 7, SP1, 64-bit OS) so I installed Cygwin-64
to run the optseq2. What I've done so far:
- Downloaded optseq2.exe (Cygwin version) and put this into
chmod (as many other linux/unix commands) do not return anything except
eventual errors.
Try './optseq2 --help' when you are in the optseq dierctory. Else write the
full path before optseq2.
Pål
Pål G. Larsson M.D., Dr. philos.
Head of Clinical Neurophysiology
Department of Neurosurgery
Hi Ines
sorry, this was my mistake. The command is mris_anatomical_stats NOT
mris_anatomical_thickness. If your SUBJECTS_DIR is set properly, you can
run:
mris_anatomical_stats -l $SUBJECTS_DIR/$subject/label/$hemi.cortex \
$subject $hemi
where $hemi is lh or rh and $subject is the
Hi Pietro
it's tough to tell from a single slice, but I would guess that the wm of
the superior temporal gyrus isn't well segmented resulting in a topological
defect that cuts it off. Can you put control points in the wm there? Look
in the wm.mgz and see if the gyrus connects and disconnects
Hi Doug, I am re-running my analysis again as I realized that there are two
subjects in my dataset who shouldn't have been included in analysis.
However, when I run the doss model I get a warning: 'unrecognized
mri_glmfit cmd option doss' but the simulations seem to be running. I have
searched
yes, you can ignore that.
doug
On 8/12/13 9:45 AM, Sinead Kelly wrote:
Hi Doug, I am re-running my analysis again as I realized that there
are two subjects in my dataset who shouldn't have been included in
analysis. However, when I run the doss model I get a warning:
'unrecognized mri_glmfit
Hi there,
Please ignore my earlier question. The Cygwin is still a mystery to me but I
have managed to run the optseq2 on a UNIX computer.
It seems there is no way to input jittered ITI and null trials at the same time
in optseq2, is this right? This is because null trials by definition is
Hi,
Linux jjanssen 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
command:
mri_glmfit-sim --glmdir lh.thickness.20 --cache 2.0 pos
error:
ERROR: thresh = 1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
i saw 1 prior email about this error message but no
Thank you very much Bruce.
I'll have a try and let you know.
Best,
Pietro
2013/8/12 Bruce Fischl fis...@nmr.mgh.harvard.edu
Hi Pietro
it's tough to tell from a single slice, but I would guess that the wm of
the superior temporal gyrus isn't well segmented resulting in a topological
use 1.3 not 1,3
On 08/12/2013 10:44 AM, joost janssen wrote:
Hi,
Linux jjanssen 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 UTC
2013 x86_64 x86_64 x86_64 GNU/Linux
command:
mri_glmfit-sim --glmdir lh.thickness.20 --cache 2.0 pos
error:
ERROR: thresh = 1,3, must be 1.3, 2.0,
Hi Steve, the PSD window is the assumed length of the hemodynamic
response and mostly unrelated to the timing of you paradigm. You need to
control the duration (part of --ev), and --tnullmin and --tnullmax. I
think that will get you where you need to be.
doug
On 08/12/2013 10:21 AM,
Hello,
I am using freesurfer 5.3 and try to run:
preproc-sess -s session1 -surface self lhrh -fsd bold -mni305 -fwhm 5
-per-session
it gives me an error:
1/1 session1
1/1 session1 003 lh -
Mon Aug 12 11:21:09 EDT 2013
ERROR: could not determine file for
Hello everyone,
isthere a method to verify which was the last version of FreeSurfer that
was used to perform the recon-all ?
For. ex. in /subjects/subject_name/scripts/build-stamp.txt/I can see
that this subject was registered the first time with FS version 5.0but
after that, an additional
Just an update!
FS 5.3 gives me the same error even when running -per-run.
Using FS 5.1, the same error pops up only in -per-session and -per-run works
fine.
Thank you in advance.
From: freesurfer-boun...@nmr.mgh.harvard.edu
Dear Freesurfer users,
I used freesurfer to extract the cortical thickness of several regions, which
are saved in the aparc.a2009s.stats text file.
To create a mask of this regions for further analyzes I used the command line:
mri_binarize --i aparc+aseg.mgz --min number --max number -- o
Hi there,
I am doing manual edits on the brainmask.mgz, wm.mgz, and
brain.finalsurfs.manedit.mgz volumes and adding control points. What
autorecon flag or from which stage of processing should I rerun recon-all
such that all of these manual edits are respected?
Thanks,
Jason
--
Jason A.
Hi Jason
-autorecon2-cp -autorecon3 should do it
cheers
Bruce
On Mon, 12 Aug 2013, Jason Tourville wrote:
Hi there,I am doing manual edits on the brainmask.mgz, wm.mgz, and
brain.finalsurfs.manedit.mgz volumes and adding control points. What
autorecon flag or from which stage of processing
Hi Doug,
I was running the command out of the $SUBJECTS_DIR. I created a log folder
in the $SUBJECTS_DIR and then the command ran smoothly! Thanks!
Best,
Alex
Hi Alex, are you running it from the project folder? It is looking for a
folder called log in the current directory. It should be
Hi,
I just wanted to confirm that label hippocampus in the hippocampal
subfields segmentation is simply parts of the hippocampus that do not fall
into one of the other major categories? Also, where can I find the units
for the hippocampal subfields? I am seeing some discrepancy between the
left
Hi Sal,
yes, the label hippocampus corresponds to the tail.
The units for the segmentation are voxels of the subfield segmentation.
Since these voxels are cubes with a .5mm side, you need to divide the
volumes by 8 to convert to cubic mm.
Cheers,
/Eugenio
On 08/12/2013 09:13 PM, Salil Soman
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