Re: [Freesurfer] permission denied

Hi Z K, Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one installed with the latest freesurfer version did not work while others finished the processing in a reasonable processing time and I got the results. Also, I have a PC at my office installed with the latest freesur

Re: [Freesurfer] adding insula voxels

I uploaded one when I sent the first email, did you receive it? Uploaded to: ftp.nmr.mgh.harvard.edu ; cd transfer/incoming The file was titled ‘mezher_insula_fail.tar.gz’ which contains the entire FS folder for one subject. Should I go ahead and resend it? Thanks!_

Re: [Freesurfer] adding insula voxels

Can you send us an image? > On Oct 30, 2014, at 7:48 PM, Adam Mezher wrote: > > > I believe it's in the surfaces. It is apparent when I load the lh.pial and > lh.white over the brainmask. > > thanks, > Adam > ___ > Freesurfer mailing list > Freesu

Re: [Freesurfer] adding insula voxels

I believe it's in the surfaces. It is apparent when I load the lh.pial and lh.white over the brainmask. thanks, Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati

Re: [Freesurfer] Longitudinal prediction

right ! I totally forgot about this ! Thank you Martin ! Sincerely,Alex  On Thursday, October 30, 2014 3:33 PM, Martin Reuter wrote: Hi Alex, the QDEC output (text in the terminal) should have the command line that was used to call the mri_glmfit command. Best, Martin

[Freesurfer] Converting lesion volume to surface area

Hello, Previously we have used a lesion of 128 microliters and have filtered out anything smaller in volume than that for analyses (single subject "pothole" analysis). Now we want to do something similar on the surface. So we need to approximate the surface area of that 128 microliters when trans

Re: [Freesurfer] Longitudinal prediction

Hi Alex, the QDEC output (text in the terminal) should have the command line that was used to call the mri_glmfit command. Best, Martin On 10/30/2014 03:08 PM, Alex Hanganu wrote: Hi Martin, could you please confirm whether the glm analysis was correctly performed ? the command line is:

Re: [Freesurfer] Longitudinal prediction

Hi Martin, could you please confirm whether the glm analysis was correctly performed ? the command line is:mri_glmfit --glmdir DIR --y lh.thickness-pc1.stack.fwhm15.mgh --label lh.fsaverage.cortex.label --fsgd FSGD_FILE --C Contrast-010..0.mtx --surf fsaverage lh  I get results, but I when I do t

[Freesurfer] Senior Researcher position in Madrid, Spain

Notification of the “Isaac Peral” Program to contract one senior researcher associated with BBVA Foundation-UPM Industry-Academia chairs for scientific-technological research in Medical Imaging, within Marie Curie Action COFUND. This notice provides for a maximum of one position in the area of

[Freesurfer] Fwd:

Notification of the “Isaac Peral” Program to contract one senior researcher associated with BBVA Foundation-UPM Industry-Academia chairs for scientific-technological research in Medical Imaging, within Marie Curie Action COFUND. This notice provides for a maximum of one position in the

Re: [Freesurfer] Error with asegstats2table function

You are in a folder that you do not have write permission to. Try cding to a different folder, or spec a path to a folder where you have write permissions, eg, asegstats2table --subjects 004 008 --meas volume --tablefile /tmp/aseg_stats.txt doug On 10/30/2014 08:28 AM, Claire Morley wrote:

Re: [Freesurfer] permission denied

Try this chmod -R a+x freesurfer/bin/* On 10/30/2014 06:27 AM, Ali Radaideh wrote: > It does not work. This is really strange > > On Thu, Oct 30, 2014 at 12:53 AM, Z K > wrote: > > I beleive it should have a lower case X, as in: > > chmod -R a+x frees

Re: [Freesurfer] Unknown problem with fsgd file

The problem is that the class name exceeds the maximum number of characters. For some strange reason I set that to be 50 and the class name is 55. I've changed it in our code tree, but you'll just have to shorten the name and it should work. doug On 10/29/2014 07:15 PM, Bronwyn Overs wrote:

Re: [Freesurfer] permission denied

Ali, First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are working properly? I am under the impression that versions of freesurfer pre-version 5.3 will not work on newer linux distributions? In regards to your current permision denied issue... What happens if you try and run tkme

Re: [Freesurfer] Name external disk not recognized

Yes, works!!! Thank you Ruthger Righart Le 2014-10-30 15:36, Douglas Greve a écrit : > can you make a symbolic link (ln -s) to the disk and then reference the > symlink instead of the direct path? > > On 10/30/14 10:33 AM, Righart, Ruthger wrote: >> Dear Freesurfers, >> >> Not sure if my questio

Re: [Freesurfer] Name external disk not recognized

Cheap solution, use backticks to evaluate the string, e.g. --reg /`echo $f1`/fsreg.dat On 30.10.2014 15:33, Righart, Ruthger wrote: > Dear Freesurfers, > > Not sure if my question is at the right place here but I'll give it a > try. > I have a memory disk with white spaces in the name: Se

Re: [Freesurfer] Name external disk not recognized

can you make a symbolic link (ln -s) to the disk and then reference the symlink instead of the direct path? On 10/30/14 10:33 AM, Righart, Ruthger wrote: > Dear Freesurfers, > > Not sure if my question is at the right place here but I'll give it a > try. > I have a memory disk with white spaces i

Re: [Freesurfer] Venous system on 3D models

You can also use bbregister to register the CT to the anatomical. I'm not sure what steps beyond that you'd need to do. doug On 10/29/14 10:47 PM, Zachary Greenberg wrote: Rich, You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for matlab, and freesurfer. First run recon-all on

[Freesurfer] Name external disk not recognized

Dear Freesurfers, Not sure if my question is at the right place here but I'll give it a try. I have a memory disk with white spaces in the name: Seagate Expansion Drive. There is no simple way to rename the disk on my Linux machine. In Unix shell scripting problems with finding the directory ca

Re: [Freesurfer] adding insula voxels

Hi Adam underestimated the insula in the aseg or in the surfaces? cheers Bruce On Wed, 29 Oct 2014, Adam Mezher wrote: Hi Bruce, Sorry for not clarifying. A number of subjects in our set have underestimated insula (usually anatomical right insula but sometimes both). I just uploaded an ex

[Freesurfer] Error with asegstats2table function

Hello Freesurfer Experts, Thanks so much again for all of your help. I am trying to complete the Anatomical ROI Analysis Tutorial because I will need to use segmentation volumes for an experiment we`re running in the lab. In particular, I am trying to complete the group stats files part of the tuto

Re: [Freesurfer] permission denied

It does not work. This is really strange On Thu, Oct 30, 2014 at 12:53 AM, Z K wrote: > I beleive it should have a lower case X, as in: > > chmod -R a+x freesurfer/bin > > -Zeke > > On 10/28/2014 01:19 AM, Ali Radaideh wrote: > > Dear Douglas > > > > Thanks for your reply. unfortunatey I still g