Re: [Freesurfer] Permission denied error from -localGI

That is weird -- ft_read_mri is not one of our files. Can you send the command line and the *full* terminal output? The lGI stuff is pretty old and does not have a maintainer. On 2/26/2024 1:40 PM, Michael Ruvalcaba wrote: External Email - Use Caution Hi Douglas, Yes I can

Re: [Freesurfer] Permission denied error

External Email - Use Caution Hello Adam, I hope you saw the previous email I sent you about changing SUBJECTS_DIR to be different from the default. Just wondering if you did that for SUBJECTS_DIR before running the recon-all. - R. On Nov 23, 2022, at 23:13, Adam Tartaglia

[Freesurfer] Permission denied error

External Email - Use Caution Hello, Immediately after running recon-all, I get an error that says cannot create directory, permission denied. I am not sure as to why this is happening. My license is in the correct location. Thank you for your time, - Adam

Re: [Freesurfer] Permission denied error from -localGI

Just closing this thread: we have solved it in https://forum.freesurfer.net/t/permission-denied-error-from-localgi/62 Thanks, Tashrif ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Permission denied error from -localGI

exist? If so what are its perms? From: Billah, Tashrif Sent: Friday, April 29, 2022 3:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Permission denied error from -localGI Thank you Douglas. We took our time to install FreeSurfer 7.2 and ret

Re: [Freesurfer] Permission denied error from -localGI

Does that file exist? If so what are its perms? On 4/29/2022 3:53 PM, Billah, Tashrif wrote: Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. However, we ran into the same error: >> reading filled volume... /bin/bash: /scratch/tp7785365264536.load_mgh.m.mgh:

Re: [Freesurfer] Permission denied error from -localGI

Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. However, we ran into the same error: >> reading filled volume... /bin/bash: /scratch/tp7785365264536.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp7785365264536.load_mgh.m.mgh for reading

Re: [Freesurfer] Permission denied error from -localGI

Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. However, we ran into the same error: >> reading filled volume... /bin/bash: /scratch/tp7785365264536.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp7785365264536.load_mgh.m.mgh for reading

Re: [Freesurfer] Permission denied error from -localGI

Can you just try it with 7.2? We had some problems at one point with temporary files in lGI that were fixed with 7.2 On 4/27/2022 9:36 AM, Billah, Tashrif wrote: Sorry about missing your earlier question--our FreeSurfer is 7.1.0 We still need your help with this issue. Thank you, Tashrif  

[Freesurfer] Permission denied error from -localGI

Sorry about missing your earlier question--our FreeSurfer is 7.1.0 We still need your help with this issue. Thank you, Tashrif Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700 === What version of FS are you running? On 3/20/2022 8:47 PM, Billah, Tashrif wrote: It

Re: [Freesurfer] Permission denied error from -localGI

What version of FS are you running? On 3/20/2022 8:47 PM, Billah, Tashrif wrote: It does not exist and cannot be created in a shared cluster. Is there a way to define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh? === Douglas N. Greve Wed, 09 Mar 2022

[Freesurfer] Permission denied error from -localGI

It does not exist and cannot be created in a shared cluster. Is there a way to define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh? === Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800 Do you have permission to /scratch? Does it exist? === Billah,

Re: [Freesurfer] Permission denied error from -localGI

Do you have permission to /scratch? Does it exist? On 3/2/2022 9:50 AM, Billah, Tashrif wrote: Hi all, We are trying to run recon-all with -localGI but running into an unknown permission denied error: $ recon-all -s sub-1001 -localGI ```

[Freesurfer] Permission denied error from -localGI

Hi all, We are trying to run recon-all with -localGI but running into an unknown permission denied error: $ recon-all -s sub-1001 -localGI ```

Re: [Freesurfer] Permission denied mri_surf2surf

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

[Freesurfer] Permission denied mri_surf2surf

External Email - Use Caution Dear experts, I created a loop for mri_surf2surf so that it would run for 300+ subjects. For most of them, it ran successfully. However, it did not work for 30 subjects. I then went to investigate one by one and I am getting a Permission denied

Re: [Freesurfer] Permission denied error with mri_surfcluster command

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

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

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

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

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

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

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

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

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

[Freesurfer] Permission denied error with mri_surfcluster command

Dear experts, I am trying to use the cluster thresholding command for my freesurfer LME outputs as referred to here . Any feedback or comments would be greatly appreciated. I am aware that there have been permission denied

Re: [Freesurfer] Permission denied error with mri_surfcluster command

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

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

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

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

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

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

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

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

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

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

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

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

[Freesurfer] permission denied

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 version freesurfer 5.3.0 does not allow me to run any command and everytime I

Re: [Freesurfer] permission denied

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

[Freesurfer] Permission denied

Dear FS team, I dowloaded the latest ML version of FS and tried to run a subject.But this error is coming up.Any suggestions? chikkuvarghese$ recon-all -i /Users/chikkuvarghese/Desktop/BL/raw/image1 -autorecon-all -s BL1 mkdir: /Applications/freesurfer/subjects/BL1: Permission denied

Re: [Freesurfer] Permission denied

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  

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

Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

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

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

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

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

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

[Freesurfer] Permission denied

Hello, 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. Thanks, Arvind ___ Freesurfer mailing list

Re: [Freesurfer] Permission denied

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