External Email - Use Caution
Hi,
I have my trac-all up and running with no error with individual subjects when I set the subject directory to individual subjects. as follow: set SUBJECTS_DIR=/*/subjects/SUBJ1 set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2) set baselist = (SUBJ1_base SUBJ1_base)
However, when I put subjects together and set the directory to multiple subjects as follow: set SUBJECTS_DIR=/*/subjects set subjlist = (SUBJ1/SUBJ1_ses-1 \ SUBJ1/SUBJ1_ses-2 \ SUBJ2/SUBJ2_ses-1 \ SUBJ2/SUBJ2_ses-2 \ etc. ) set baselist = (SUBJ1/SUBJ1_base \ SUBJ1/SUBJ1_base \ SUBJ2/SUBJ2_base \ SUBJ2/SUBJ2_base \ etc.)
It has a problem finding the baselist file: "cannot find /*/subjects/SUBJ1/SUBJ1_ses-1.long.SUBJ1/SUBJ1_base". Should I copy SUJB1_base under the SUBJ1.long.SUBJ1 and run it again? Why is it not happening with the subject individual?
Best, Qi
You cannot have multiple SUBJECTS_DIR's. It is supposed to be the base directory under which all subjects' dirs are saved. You could have a different configuration file for each subject if you want each of them to have a different SUBJECTS_DIR, but this hack won't work for longitudinal analyses as all the time points from the same subject have to be defined in the same config file. If you must have subjects saved in different locations, you can create a "mock" SUBJECTS_DIR and in it create symlinks to the dirs of every individual subject (this includes both *.long.* and base dirs). ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Qi qi.zeng@icahn.mssm.edu Sent: Thursday, April 30, 2020 3:40 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] longitudinal dmrirc script error with the baselist
External Email - Use Caution
Hi,
I have my trac-all up and running with no error with individual subjects when I set the subject directory to individual subjects. as follow: set SUBJECTS_DIR=/*/subjects/SUBJ1 set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2) set baselist = (SUBJ1_base SUBJ1_base)
However, when I put subjects together and set the directory to multiple subjects as follow: set SUBJECTS_DIR=/*/subjects set subjlist = (SUBJ1/SUBJ1_ses-1 \ SUBJ1/SUBJ1_ses-2 \ SUBJ2/SUBJ2_ses-1 \ SUBJ2/SUBJ2_ses-2 \ etc. ) set baselist = (SUBJ1/SUBJ1_base \ SUBJ1/SUBJ1_base \ SUBJ2/SUBJ2_base \ SUBJ2/SUBJ2_base \ etc.)
It has a problem finding the baselist file: "cannot find /*/subjects/SUBJ1/SUBJ1_ses-1.long.SUBJ1/SUBJ1_base". Should I copy SUJB1_base under the SUBJ1.long.SUBJ1 and run it again? Why is it not happening with the subject individual?
Best, Qi
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
External Email - Use Caution
Hi Anastasia,
I think there are some misunderstandings here. I have created one configuration file for each subject and it works processing longitudinal data. And since all my subjects are stored following /subjects/ in one directory, I assumed adding individual 'SUBJ1/' to the file would work. Here attached my individual and multiple subjects' configuration file. Can you help take a look? From what you say, I have some suspicion that my individual configuration could also have some problem. Thank you so much !
Best, Qi
On Thu, Apr 30, 2020 at 4:41 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
You cannot have multiple SUBJECTS_DIR's. It is supposed to be the base directory under which all subjects' dirs are saved. You could have a different configuration file for each subject if you want each of them to have a different SUBJECTS_DIR, but this hack won't work for longitudinal analyses as all the time points from the same subject have to be defined in the same config file. If you must have subjects saved in different locations, you can create a "mock" SUBJECTS_DIR and in it create symlinks to the dirs of every individual subject (this includes both *.long.* and base dirs).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < qi.zeng@icahn.mssm.edu> *Sent:* Thursday, April 30, 2020 3:40 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] longitudinal dmrirc script error with the baselist
External Email - Use CautionHi,
I have my trac-all up and running with no error with individual subjects when I set the subject directory to individual subjects. as follow: set SUBJECTS_DIR=/*/subjects/SUBJ1 set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2) set baselist = (SUBJ1_base SUBJ1_base)
However, when I put subjects together and set the directory to multiple subjects as follow: set SUBJECTS_DIR=/*/subjects set subjlist = (SUBJ1/SUBJ1_ses-1 \ SUBJ1/SUBJ1_ses-2 \ SUBJ2/SUBJ2_ses-1 \ SUBJ2/SUBJ2_ses-2 \ etc. ) set baselist = (SUBJ1/SUBJ1_base \ SUBJ1/SUBJ1_base \ SUBJ2/SUBJ2_base \ SUBJ2/SUBJ2_base \ etc.)
It has a problem finding the baselist file: "cannot find /*/subjects/SUBJ1/SUBJ1_ses-1.long.SUBJ1/SUBJ1_base". Should I copy SUJB1_base under the SUBJ1.long.SUBJ1 and run it again? Why is it not happening with the subject individual?
Best, Qi
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Qi - "Subject IDs" should be just subject IDs (a.k.a. subject names), not paths to subject directories. So one of the config files that you attached should work, but the other should not.
a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Qi qi.zeng@icahn.mssm.edu Sent: Thursday, April 30, 2020 5:03 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal dmrirc script error with the baselist
External Email - Use Caution
Hi Anastasia,
I think there are some misunderstandings here. I have created one configuration file for each subject and it works processing longitudinal data. And since all my subjects are stored following /subjects/ in one directory, I assumed adding individual 'SUBJ1/' to the file would work. Here attached my individual and multiple subjects' configuration file. Can you help take a look? From what you say, I have some suspicion that my individual configuration could also have some problem. Thank you so much !
Best, Qi
On Thu, Apr 30, 2020 at 4:41 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: You cannot have multiple SUBJECTS_DIR's. It is supposed to be the base directory under which all subjects' dirs are saved. You could have a different configuration file for each subject if you want each of them to have a different SUBJECTS_DIR, but this hack won't work for longitudinal analyses as all the time points from the same subject have to be defined in the same config file. If you must have subjects saved in different locations, you can create a "mock" SUBJECTS_DIR and in it create symlinks to the dirs of every individual subject (this includes both *.long.* and base dirs). ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Sent: Thursday, April 30, 2020 3:40 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] longitudinal dmrirc script error with the baselist
External Email - Use Caution
Hi,
I have my trac-all up and running with no error with individual subjects when I set the subject directory to individual subjects. as follow: set SUBJECTS_DIR=/*/subjects/SUBJ1 set subjlist = (SUBJ1_ses-1 SUBJ1_ses-2) set baselist = (SUBJ1_base SUBJ1_base)
However, when I put subjects together and set the directory to multiple subjects as follow: set SUBJECTS_DIR=/*/subjects set subjlist = (SUBJ1/SUBJ1_ses-1 \ SUBJ1/SUBJ1_ses-2 \ SUBJ2/SUBJ2_ses-1 \ SUBJ2/SUBJ2_ses-2 \ etc. ) set baselist = (SUBJ1/SUBJ1_base \ SUBJ1/SUBJ1_base \ SUBJ2/SUBJ2_base \ SUBJ2/SUBJ2_base \ etc.)
It has a problem finding the baselist file: "cannot find /*/subjects/SUBJ1/SUBJ1_ses-1.long.SUBJ1/SUBJ1_base". Should I copy SUJB1_base under the SUBJ1.long.SUBJ1 and run it again? Why is it not happening with the subject individual?
Best, Qi
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
freesurfer@nmr.mgh.harvard.edu
-
Yendiki, Anastasia -
Zeng, Qi