Dear experts,
I extracted the 3 mgz volumes of the GCA file used in the recon-all process
(RB_all_2008-03-26.gca). I modified these files and I wanted to recreate the
GCA file by reunite the 3 mgz. I tried some mri_convert command but I failed to
convert these 3 volumes in 1 GCA file. Is it pos
Hallo all,
I have installed freesurfer v5.3 on Ubuntu 12.04 LTS. The GCC version is 4.6. I
use the recon-all using -all and -openmp option. I observed that openmp does
not seem to have any effect in the execution of freesurfer. I verified the
installation of openmp using dpkg --status libgomp1
Hi Krishnaprasad
what is your full recon-all command line? And how do you know it isn't
working? Have you tried running "top" during the mri_ca_register stage?
The upcoming (one of these months!) release will have much more in the
way of openmp optimization
cheers
Bruce
On Mon, 12 Jan 2015
Hi Raunak
it isn't a straight (binary) mask - it's a label map. You can use it to
determine what voxels are in e.g. the left hippocampus (label == 17) then
use the norm.mgz to compute the intensity co-occurrence map
cheers
Bruce
On Mon, 12 Jan
2015, Raunak Mundada wrote:
Hi Bruce
I am a
Hi Sophie
what kind of modifications did you make? The 3 volumes are part of the
information in the gca, but not all of it (they don't contain the markov
information) so there is no way to recreate it from only them. mri_ca_train
is the only way to make a gca at the moment, although there is s
Hi Christina
I think this is something that is fixed in the new version. If you want a
patch we can send you new versions of recon-all and mris_make_surfaces
cheers
Bruce
On
Sat, 10 Jan 2015, Christina Chen wrote:
On Dec 24, 2014, at 10:44 PM, Christina Chen wrote:
> Hi!
>
> When looking
does that dicom exist? Can you run ls -l on it?
On Sat, 10 Jan 2015,
Borzello, Mia wrote:
> I just fixed that but I'm still getting an error. I attached a screenshot.
>
> Thanks,
> Mia
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...
Hi Bruce,
Thanks for your reply. May be I should not have said it is not working. Sorry
for that.
The command that I used was "recon-all -i
/usr/local/freesurfer/subjects/bert/mri/T1.mgz -subjid exampledata1 -all
-openmp 8".
Yeah, I observed the core usage using htop until the end of first min
yes, in 5.3 there is only openmp support in a couple of binaries. Those
stages are reached maybe 15 minutes into recon-all depending on your
hardware.
cheers
Bruce
On Mon, 12 Jan 2015, Narayanan,
Krishnaprasad wrote:
Hi Bruce,
Thanks for your reply. May be I should not have said it is not
Yeah, it works. I am able to see the load on multi cores.
Regards,
Krishnaprasad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Montag, 12. Januar 2015 14:51
To: Freesurfer support list
Subj
You need to have matlab in your path to run selxavg3-sess (octave should
work as well)
On 01/10/2015 07:08 PM, std...@virgilio.it wrote:
> Hi list,
>
> the selxavg3-sess -s Sess01 -a fc.lpccseed.surf.lh in fcMRI analysis
> produces this error.
>
>
> rawfunc2surf-sess completed
>
> --
I guess just delete what you have and redownload and reinstall
On 01/11/2015 08:05 PM, Muhammad Naveed Iqbal Qureshi wrote:
> No, I have more than 200GB free space available, I think the
> freesurfer installation is corrupted, how can I update it?
>
> *Best Regards,*
> *Muhammad Naveed Iqbal Qures
Can you send mask_registered.nii.gz through our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 01/09/2015 08:58 PM, Eunice Yang wrote:
> Hello- I am trying to compute the proportion of different tissue types within
> an ROI using a mask:
> mri_segstats --seg aseg.auto.mgz --mask mask
Muhammad,
Please send me the recon-all.log file for this subject. It should be
found in:
/media/sf_Dataset/ADHD200/Processed/scripts/recon-all.log
Thanks.
-Zeke
On 01/04/2015 07:56 PM, Muhammad Naveed Iqbal Qureshi wrote:
> Dear community,
>
> I execute the following command:
>
> recon-all -i
Hi Anastasia,
Thank you for your response. I have made the changes that you recommended and
attempted to run trac-all -prep on one of the subjects with errors. I am now
getting the following error:
Writing output files to
/home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.
Can you please attach the entire trac-all.log file? It's hard to tell just
from the last few lines, the initial error may have happened much earlier.
On Mon, 12 Jan 2015, Worker, Amanda wrote:
> Hi Anastasia,
>
> Thank you for your response. I have made the changes that you recommended and
> a
glad to hear it
Bruce
On Mon, 12 Jan 2015, Narayanan, Krishnaprasad wrote:
Yeah, it works. I am able to see the load on multi cores.
Regards,
Krishnaprasad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruc
Have you checked that the registration has been fixed? It looks like it
might not.
On Mon, 12 Jan 2015, Worker, Amanda wrote:
> Yes of course. Please find attached.
>
> Thanks,
>
> Amanda
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of
Hello,
I am currently trying to visualize group differences in cortical thickness
across subject groups. In addition to using the qdec GUI, I am playing with the
make_average_surface command as well as the make_average_subject command to
then visualize in freeview or tksurfer - though I'm quite
Hi Gabriella
make_average_subject calls make_average_surface (and
make_average_volumes I believe). You probably want to use
make_average_subject and let it do what it wants to (that is, let it make
everything it knows how to, both surfaces and volumes)
cheers
Bruce
On Mon, 12 Jan 2015, Hirsc
Hi Doug- I uploaded an example mask. According to fslstats it has 29016 voxels
whereas mri_segstats suggests it has 26182 voxels.
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=6sthhn0ld2p
Thanks!
Eunice
On Jan 12, 2015, at 8:19 AM, Douglas N Greve wrote:
>
> Can you send mask_registered.nii.gz
The problem is that your mask is not a mask. A mask should have binary
values (ie, either 0 or 1). Yours has values in-between. mri_segstats
sets the threshold to 0.5 which gives 26526 voxels. FSL is probably
using a threshold very close to 0.
doug
On 01/12/2015 04:25 PM, Eunice Yang wrote:
My binary mask was originally made in native space so when I transformed it
into freesurfer (conformed) space, it must have interpolated the edge of the
mask to produce values between 0 and 1. Thank yo so much for clearing that up.
Eunice
On Jan 12, 2015, at 1:49 PM, Douglas N Greve wrote:
>
Hi Zeke,
Please find the attached log file.
Thanks
Best Regards,
Muhammad
Naveed Iqbal Qureshi
P please don't print this e-mail unless
you really need to
> Date: Mon, 12 Jan 2015 11:33:29 -0500
> From: zkauf...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu; mniqure...@hotmail
Okay, just ran ls-l and don't see it- image attached.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, January 12, 2015 8:39 AM
To: Freesurfer support
Hi Mia
you need to run it with the full path of the dicom you are trying to give
to recon-all
cheers
Bruce
On Tue, 13 Jan 2015,
Borzello, Mia wrote:
> Okay, just ran ls-l and don't see it- image attached.
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
Hi Bruce,
Thanks for e-mail. I did a search on the dicom file, and it said there was no
file (top part of image). However, I can get myself in the folder and the
dicome "4571157" is in there. I'm wondering if it's a file type issue. The
files aren't listed as 4571157.dcm for example- could tha
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