Dear Freesurfer expert,
I am using Freesurfer version 5.1.0.
I am dealing with some problems with recon_checker command.
I cannot open the html file to see the figures. The command generates the
images but they are not saved.
It is written that:
*converting snapshots to tiff and making html page..
Hi Efrat,
You need to install ImageMagick Studio version 6.2.8 or higher. See
website below for downloading.
http://www.imagemagick.org/script/index.php
-Louis
On Thu, 1 Nov 2012, Efrat Kliper wrote:
Dear Freesurfer expert,
I am using Freesurfer version 5.1.0.
I am dealing with some prob
Hi Doug,
The subject name for structural is "SUBJ1" when I did recon-all, which is also
the content of file "subjectname". My dir structures of "structural" and
"retinotopy" are the same as http://www.alivelearn.net/?p=65 . "SUBJ1" is
stored under "structural". if I set SUBJECTS_DIR as "..
Try using this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fieldsign-sess
doug
On 11/01/2012 11:47 AM, Zhou, Wei wrote:
> Hi Doug,
>
> The subject name for structural is "SUBJ1" when I did recon-all, which
> is also the content of file "subjectname". My dir structures
Dear all,
Is there a way to crop a surface in FS, freeview or matlab? I have the
inner_skull_surface in BEM folder, and I want to see just the right half,
akin to cropping along the A (RAS) axis from the left. This is in order to
visualize the inside of the surface with some electrode applications
Hi Octavian
sure, define a sagittal cutting plane in tksurfer, or in matlab set
ripflag=1 for all vertices with the x coord > 0 (or < 0)
cheers
Bruce
On Thu, 1 Nov 2012,
octavian lie wrote:
Dear all,
Is there a way to crop a surface in FS, freeview or matlab? I have the
inner_skull_surf
Thank you, Bruce. Is seems that the cut works well in tksurfer, however I
am unable to save the cut surface, if I use save or save as, it saves the
original (whole) surface. What should I do?
Octavian.
On Thu, Nov 1, 2012 at 11:49 AM, Bruce Fischl wrote:
> the easiest thing would be to copy it in
save it as a patch
On Thu, 1 Nov 2012, octavian lie wrote:
Thank you, Bruce. Is seems that the cut works well in tksurfer, however I am
unable to save the cut surface, if I use save or
save as, it saves the original (whole) surface. What should I do?
Octavian.
On Thu, Nov 1, 2012 at 11:49 AM,
Doug,
I tried running mri_glmfit-sim without the --bg flag and it finished in
10 minutes without any errors. This has never happened before, so I highly
suspect these results. Do you know what could be wrong? In case you need
it, the summary file output and terminal output are attached.
-Rya
Dear Bruce,
One last question. I saved the cut surface as rh.inner-skull-surface
(original was rh.sub_inner_skull_surface) as a patch, but when trying to
see it in tksurfer, I get the following error message:
tksurfer sub rh inner-skull-surface
subject is sub
hemi is rh
surface is inner-skull-surf
It is no longer a surface - it is a patch and you need to load it that way.
It's a different file format
Bruce
On Nov 1, 2012, at 1:22 PM, octavian lie wrote:
> Dear Bruce,
> One last question. I saved the cut surface as rh.inner-skull-surface
> (original was rh.sub_inner_skull_surface) as a
Can you send the command line and attach the files?
thanks
doug
On 11/01/2012 01:11 PM, Ryan wrote:
> Doug,
>I tried running mri_glmfit-sim without the --bg flag and it
> finished in 10 minutes without any errors. This has never happened
> before, so I highly suspect these results. Do you kn
Well, that is funny. Now it has finished without errors. I am not quite
sure what happened. The command line was the same both times: recon-all
-make all -subjid CON1
Is it possible that some other process that was going on on our server
caused the processing for this subject to end abnormally? We
how much ram do you have?
On Thu, 1 Nov 2012, Christine Smith wrote:
Well, that is funny. Now it has finished without errors. I am not quite sure
what happened. The command line was the same both times: recon-all -make all
-subjid CON1
Is it possible that some other process that was going on on
Doug,
Here are the files.
On Thu, Nov 1, 2012 at 2:00 PM, Douglas N Greve
wrote:
> Can you send the command line and attach the files?
> thanks
> doug
>
>
> On 11/01/2012 01:11 PM, Ryan wrote:
>
>> Doug,
>>I tried running mri_glmfit-sim without the --bg flag and it finished
>> in 10 minut
The problem is that the fwhm is not-a-number (glmdir/fwhm.dat). Usually
this means that there is something messed up with the mask
(glmdir/mask.mgh). View the mask to see what is up
tksurfer fsaverage lh inflated -ov glmdir/mask.mgh -fminmax .5 1
doug
On 11/01/2012 02:39 PM, Ryan wrote:
> Doug,
Dear Bruce,
Thank you for your assist.
I see the difference between patch and surface, but I would need to get he
cut surface in matlab. I do not know how to set the ripflag=1 for x<0.
Here is the code I use to upload surfaces in Matlab:
function [vertex_coords, faces] = read_surf(fname)
%QUAD_F
you should be able to use the read_patch.m that is in our matlab dir
cheers
Bruce
On Thu,
1 Nov 2012, octavian lie wrote:
Dear Bruce,
Thank you for your assist.
I see the difference between patch and surface, but I would need to get he
cut surface in matlab. I do not know how to set the rip
I'm using Freesurfer version 5.1.0 and recon-all keeps exiting with errors
during the intensity correction step. The error reads:
Writing to ./tmp.mri_nu_correct.mni.24988/output.mean.dat
(standard_in) 1: syntax error
mris_calc -o ./tmp.mri_nu_correct.mni.24988/nu2.mnc
./tmp.mri_nu_correct.mni.249
The mask looks ok to me (I did not notice anything strange around the
CC). How do the sig maps look? Is there any data set in there that is
odd? you can evaluate this with
tksurfer fsaverage lh inflated -ov glmdir/mask.mgh -fminmax .5 1-t y.mgh
this will bring up a "time" course where each poin
Hello Nick,
I've looked quite closely at the endian-ness, and I think I've got the bytes
the right way around - but still with no success :-(
I've narrowed the issue down to the dicom library calls, so this is pretty
mature and stable code. I would think that it should compile fine on the
pow
On 11/01/2012 06:35 PM, Ryan wrote:
> Doug,
>Picture 4 shows the difference between the medial surface for this
> analysis and for another type of analysis (where I created my own
> matrix file) that completed normally. Is this normal? I have never
> looked at this surface for errors befor
Hi Angie, is that disk full? You can check with the df command
doug
On 11/01/2012 04:43 PM, Angie Morales wrote:
> I'm using Freesurfer version 5.1.0 and recon-all keeps exiting with
> errors during the intensity correction step. The error reads:
>
> Writing to ./tmp.mri_nu_correct.mni.24988/outp
Thanks for the reply. Unfortunately, disk space does not seem to be the
problem.
On Thu, Nov 1, 2012 at 1:43 PM, Angie Morales wrote:
> I'm using Freesurfer version 5.1.0 and recon-all keeps exiting with errors
> during the intensity correction step. The error reads:
>
> Writing to ./tmp.mri_nu_
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