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

an we do now? -Tashrif === Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700 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:

Re: [Freesurfer] Permission denied error from -localGI

an we do now? -Tashrif Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700 === 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

[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

[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

[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 ```

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We are hiring a data engineer at Massachusetts General Hospital to visualize various human subject data through web applications. You need to be fluent in web application building. * Immediate start date * Master's degree preferred * Visa sponsorship available See details and apply

Re: [Freesurfer] orig/001.mgz to brain.mgz transformation?

freesurfer@nmr.mgh.harvard.edu Message-ID: Content-Type: text/plain; charset="utf-8" On 10/27/2021 10:58 AM, Billah, Tashrif wrote: > Hi, > > 1. What is the name of the space of wmparc.mgz? I see that it is in > the same space of brain.mgz. > Yes > > 1. > >

[Freesurfer] orig/001.mgz to brain.mgz transformation?

Hi, 1. What is the name of the space of wmparc.mgz? I see that it is in the same space of brain.mgz. 2. What transform file brings orig/001.mgz to brain.mgz? Best, Tashrif ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Hiring a web developer

The web developer will join a research laboratory at Harvard Medical School/Mass General Brigham. It is located in Boston, MA. Here is the job description: https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3161646=GMT-04%3A00=America%2FNew_York If you have any question, reach out

[Freesurfer] voxel to ras transform written by mri_convert -c

Hi there, How is the rightmost column in `mri_convert -c` calculated? I have the following fslhd (relevant fields shown only) in a NIFTI image: ``` dim1208 dim2300 dim3320 qto_xyz:1 0.7996900.022176 0.001352-86.687996 qto_xyz:2 -0.021442

[Freesurfer] recon-all output resolution

Hi all, Is the resolution of mri/*mgz files produced by `recon-all -all` always 1mm^3 regardless of the resolution of my input unless -hires is used? This is what I found in recon-all.log: without --hires: mri_convert 001/mri/rawavg.mgz 001/mri/orig.mgz --conform I believe the `--conform`

[Freesurfer] FastSurfer with FreeSurfer version 7.1.0?

Hi Barbara and Martin, I didn't have any problem running FastSurfer with FreeSurfer 7.1.0 either. Best, Tashrif ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Maintain consistency in build stamp patterns

See the build stamp patterns: In versions < 6.0.0: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c In version 7.1.0: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b The latter has "v" missing from the version string that makes it hard for my pipeline to detect FreeSurfer

[Freesurfer] Flag(s) for parallel processing

here it can The run time on that page is probably not accurate. But is it faster when you use those options? On 7/16/2020 11:47 PM, Billah, Tashrif wrote: This <https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes>says "-openmp after -parallel", this <ht

[Freesurfer] Flag(s) for parallel processing

This says "-openmp after -parallel", this says "export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2", while this says

Re: [Freesurfer] mris_fix_topology command does not finish

? -niters N stop genetic algorithm after N iterations -seed N set random number generator to seed N -s N smooth corrected surface by N iterations Cheers, Tashrif From: Billah, Tashrif Sent

Re: [Freesurfer] mris_fix_topology command does not finish

cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview -Tashrif . From: Billah, Tashrif Sent: Sunday, May 10, 2020 2:11 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Bouix, Sylvain,Ph.D

[Freesurfer] mris_fix_topology command does not finish

Hi there, The following commands part of `recon-alll -i some_T1w.nii.gz -autorecon2` does not finish for some of our data: #@# Fix Topology lh Sat May 9 14:17:52 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

or whether one of the autorecons is sufficient? On 5/1/2020 10:21 AM, Billah, Tashrif wrote: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65836.html> 2020-04-17

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

ve.com/search?l=freesurfer%40nmr.mgh.harvard.edu=subject:%22%5C%5BFreesurfer%5C%5D++Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22=newest=1> Billah, Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu=from:%22Billah%2C+Tashrif%22=newest=1&g

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

Hello Douglas, Waiting to hear back from you on my question Thanks, Tashrif ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Which autorecon uses -hippocampal-subfields flags?

Douglas, Let's try with an example. See the two ways T2 image can be integrated with recon-all Altogether: recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all autorecon3 only: recon-all -subject

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

lds> integrates the subfileds with recon-all only but do no show combination with any autorecon commands. -Tashrif . From: Billah, Tashrif Sent: Friday, April 17, 2020 1:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Which autorecon uses -hippo

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif . ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Which autorecon uses -hippocampal-subfields flags?

Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags? autorecon1, 2 , or 3? My goal is to use the flag specifically with one of the three and not with recon-all in general as shown in the above page. I do understand that the

Re: [Freesurfer] Does FS guarantee the same results if run several times?

Hi Xiaojiang and Douglas, I think it is the attribute of having random initialization in the registration steps. This slight discrepancy can also be observed with antsRegistration. I don't know the exact algorithm FreeSurfer uses for registration though. Best, Tashrif

[Freesurfer] [recon-all] [use of -T2] Does only -autorecon3 use -T2?

Hi all, Is -T2 used only in -autorecon3 as shown here: recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 In other words, if I do: recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume

[Freesurfer] Is -skullstrip set by default?

With recon-all, is [-skullstrip](https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip) option set by default? I am trying to understand why there is a separate -noskullstrip option. Best, Tashrif - Tashrif Billah,

[Freesurfer] Download link broken

Hi FreeSurfer team, The following link appears broken since 10/17 evening. https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz Can you look into it? Best, Tashrif -