Re: [Freesurfer] Permission denied mri_surf2surf

2020-09-09 Thread fsbuild
External Email - Use Caution Hello Ellen, I suspect that you really do not have the system privileges to read/write every subject directory. I have run into this with other commands that scan multiple subject directories. Assuming there is one top level directory that contains

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-03-03 Thread Douglas N Greve
All the values are between 0 and 1, so I suspect this is a map of p-values, not a map of -log10(p). Is that right? If so, convert it to -log10(p) and rerun. You can do this in matlab with p = MRIread('rh_time.mgh'); sig = p; sig.vol = -log10(abs(p.vol)); MRIwrite(sig,'sig.mgh'); On 03/03/2016

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-03-03 Thread Douglas N Greve
Can you send me rh_time_spval.mgh? On 03/01/2016 04:42 PM, Jennifer Legault wrote: > Hi Doug, > > Thank you for responding. I actually realized what was the matter (I > had specified the path for fsaverage which led to the error; this is > no longer an issue so long as I use "--subject

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-03-01 Thread Douglas N Greve
can you send your command line and terminal output? On 02/25/2016 01:52 PM, Jennifer Legault wrote: > Hi Douglas, > > Thank you for all your help. When I say "volume" I do mean the FS > thickness*area measure. I ran the mri_glmfit with --osgm and for the > FWHM received the value of .925737.

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-25 Thread Jennifer Legault
Hi Douglas, Thank you for all your help. When I say "volume" I do mean the FS thickness*area measure. I ran the mri_glmfit with --osgm and for the FWHM received the value of .925737. Assuming that this rounds up to 1, I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-11 Thread Jennifer Legault
Thank you for your response. Do I need to run the glm_fit-sim command to make the csd file? I feel this would be inappropriate for my data since I already ran the LME model. Second, is there an argument to make an output file that can be visualized via freeview? In other words, how can I view

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-11 Thread Douglas N Greve
On 02/11/2016 11:19 AM, Jennifer Legault wrote: > Thank you for your response. Do I need to run the glm_fit-sim command > to make the csd file? I feel this would be inappropriate for my data > since I already ran the LME model. No, look in $FREESURFER_HOME/average/mult-comp-cor/fsaverage.

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-11 Thread Jennifer Legault
That's very useful, thank you. In terms of FWHM, I am examining gray matter volume, not cortical thickness, and was previously instructed by Martin Reuter not to smooth these data. Do you think it would make sense then to just use the fwhm01? And in terms of the voxel-wise threshold, is there a

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-11 Thread Douglas N Greve
by "volume" do you mean a VBM-type analysis or do you mean the volume that comes out of FS (thickness*area)? If you are going to use a clusterwise correction, then you have to have a FWHM measurement. You can try analyzing it in mri_glmfit with --osgm just to get the FWHM out of it. You

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-10 Thread Douglas N Greve
I meant for the output files, so the --o in particular On 02/10/2016 01:47 PM, Jennifer Legault wrote: > Douglas, > > Thank you for your quick response. When I add --sd [path_location], I > get the following error: > Loading source values > mri_read(): couldn't determine type of file

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-10 Thread Jennifer Legault
Douglas, Thank you for your quick response. When I add --sd [path_location], I get the following error: Loading source values mri_read(): couldn't determine type of file [path_location]/rh_time_spval ERROR: could not read rh_time_spval as type Should I use another argument? Best, Jen On

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-10 Thread Jennifer Legault
Thank you very much for your help! I still received a "cannot read file type" error when I only added the path to the output --o part, however when I also added the path to the input file, it worked! I do have one more question: Which argument can I add so that in my output file I see the

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-10 Thread Douglas N Greve
Try specifying the full path to the output On 02/10/2016 12:59 PM, Jennifer Legault wrote: > Dear experts, > > I am trying to use the cluster thresholding command for my freesurfer > LME outputs as referred to here > . > Any

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-10 Thread Douglas Greve
There is a (very long) command line on that page. Mainly you need a csd file. To get that you need the FWHM of your analysis, the voxel-wise threshold, and the sign of the contrast (or abs). Then the relevant output will be the --sum. You can run it with --help to get more info. On 2/10/16

Re: [Freesurfer] permission denied

2014-11-04 Thread Robby De Pauw
Hi I’ve previously encountered the same error. I’ve also tried to change permission but that didn’t really work out for me. I have fixed it by installing libjpeg62-dev: Maybe the following command could fix your problem too? sudo apt-get install libjpeg62-dev Hope this might work for you?

Re: [Freesurfer] permission denied

2014-10-31 Thread Ali Radaideh
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

Re: [Freesurfer] permission denied

2014-10-31 Thread zkaufman
Yes, please try running as root and get back when you have the chance. This is a very odd issue and your results when running as root will provide insight. -Zeke 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

Re: [Freesurfer] permission denied

2014-10-30 Thread Ali Radaideh
It does not work. This is really strange On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu 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.

Re: [Freesurfer] permission denied

2014-10-30 Thread Z K
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

Re: [Freesurfer] permission denied

2014-10-30 Thread Douglas N Greve
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 zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: I beleive it should have a lower case X, as in:

Re: [Freesurfer] permission denied

2014-10-29 Thread Z K
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 get the same error. Here is the terminal output. Is there anything else I can do?

Re: [Freesurfer] permission denied

2014-10-27 Thread Ali Radaideh
Dear Douglas Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME

Re: [Freesurfer] permission denied

2014-10-26 Thread Douglas Greve
Try chmod -R a+X freesurfer/bin On 10/26/14 1:57 PM, Ali Radaideh wrote: Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest

Re: [Freesurfer] Permission denied

2013-03-14 Thread Bruce Fischl
you probably want to specify the SUBJECTS_DIR as being somewhere else that you have write permission to. You can do this with the -sd path on the recon-all command line, or in the environment. cheers Bruce On Thu, 14 Mar 2013, Varghese Chikku wrote: Dear FS team,I dowloaded the latest ML  

Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread Anastasia Yendiki
Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or is BA3b.thresh the only one? If you remove the .thresh do you still get an error? Thanks, a.y On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello, I ran recon-all and left it running Friday

Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread preciado
It looks like this is the first *thresh.* label that caused the problem. The following command ran and executed properly just before the error message on the log. mri_label2label --srcsubject fsaverage --srclabel

Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread Anastasia Yendiki
Probably a network glitch? I'd try restarting it and seeing if the error persists. On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: It looks like this is the first *thresh.* label that caused the problem. The following command ran and executed properly just before the error message

Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread preciado
I am thinking that that's possible. Same command with same type of parameters executed successfully before the failure, and now previously failed command is working. I will try it again... Thanks for the input. -Ronny Probably a network glitch? I'd try restarting it and seeing if the error

Re: [Freesurfer] Permission denied

2005-08-19 Thread Kevin Teich
Recently moved freesurfer from one system to another, but I am having trouble executing it. ./csurf: Permission denied. I have license in the right folder. Has anyone experienced the same problem. Make sure it is executable. Try: chmod a+x csurf -- Kevin Teich