Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?
by Billah, Tashrif 01 May '20

01 May '20

Assuming `recon-all autorecon2 ...` requires completion of `recon-all autorecon1 ...` and autorecon3 requires completion of both 1 and 2, yes, I am asking which autorecon is sufficient. -Tashrif Are you asking whether you have to run recon-all all the way through in order to run the subfields 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 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Billah, Tashrif <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Douglas, Let's try with an example. See the two waysT2 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 subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 Similar to the former, -hippocampal-subfields-T1integrated with recon-all: recon-all -all -s bert -hippocampal-subfields-T1 Now the question, compared to the latter, which autorecon[1/2/3] would accept -hippocampal-subfields-T1? Does it make sense now? -Tashrif . ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65832.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> I don't understand the question. To run recon-all through to the end implies that you have run all the -autorecons On 4/17/2020 2:53 PM, Billah, Tashrif wrote: Right, I understand the rule about the scripts. However, my original question was about the subfields -hippocampal-subfields-T1/T2/T1T2 Again, can they be run with any of the autorecons separately? The example shown here <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> 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(a)nmr.mgh.harvard.edu *Subject:* 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65829.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Billah, Tashrif <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Right, I understand the rule about the scripts. However, my original question was about the subfields -hippocampal-subfields-T1/T2/T1T2 Again, can they be run with any of the autorecons separately? The example shown here<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> 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(a)nmr.mgh.harvard.edu Subject: 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65827.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> You have to run recon-all all the way through and then run the subfield scripts separately. On 4/17/2020 12:21 PM, Douglas N. Greve wrote: None! You have to run it all the way through to the end and then run them from the command line. On 4/17/2020 11:40 AM, Billah, Tashrif wrote: Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields%C2%A0flags>? 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 new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65825.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Billah, Tashrif <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif . ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65818.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> None! You have to run it all the way through to the end and then run them from the command line. On 4/17/2020 11:40 AM, Billah, Tashrif wrote: Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields%C2%A0flags>? 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 new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65814.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Billah, Tashrif <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> 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 new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?
by Billah, Tashrif 01 May '20

01 May '20

[Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65836.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Billah, Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> 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 subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 Similar to the former, -hippocampal-subfields-T1 integrated with recon-all: recon-all -all -s bert -hippocampal-subfields-T1 Now the question, compared to the latter, which autorecon[1/2/3] would accept -hippocampal-subfields-T1? Does it make sense now? -Tashrif . ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65832.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Douglas N. Greve<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> I don't understand the question. To run recon-all through to the end implies that you have run all the -autorecons On 4/17/2020 2:53 PM, Billah, Tashrif wrote: Right, I understand the rule about the scripts. However, my original question was about the subfields -hippocampal-subfields-T1/T2/T1T2 Again, can they be run with any of the autorecons separately? The example shown here <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> 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(a)nmr.mgh.harvard.edu *Subject:* 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65829.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Billah, Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Right, I understand the rule about the scripts. However, my original question was about the subfields -hippocampal-subfields-T1/T2/T1T2 Again, can they be run with any of the autorecons separately? The example shown here<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> 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(a)nmr.mgh.harvard.edu Subject: 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(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65827.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Douglas N. Greve<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> You have to run recon-all all the way through and then run the subfield scripts separately. On 4/17/2020 12:21 PM, Douglas N. Greve wrote: None! You have to run it all the way through to the end and then run them from the command line. On 4/17/2020 11:40 AM, Billah, Tashrif wrote: 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 new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65825.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Billah, Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif . ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65818.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Douglas N. Greve<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> None! You have to run it all the way through to the end and then run them from the command line. On 4/17/2020 11:40 AM, Billah, Tashrif wrote: 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 new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65814.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Billah, Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> 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 new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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ASEG and FAST Cerebellar Segmentations
by Camille Williams 01 May '20

01 May '20

External Email - Use Caution Hi, I am currently using data from the UKBiobank (https://www.ukbiobank.ac.uk/ <https://www.ukbiobank.ac.uk/>) which has segmented its brain imaging data using Freesurfer tools (https://biobank.ctsu.ox.ac.uk/crystal/crystal/docs/brain_mri.pdf <https://biobank.ctsu.ox.ac.uk/crystal/crystal/docs/brain_mri.pdf>). I calculated the sum of the FAST cerebellar grey matter volumes and compared them to the sum of the ASEG cerebellar cortex volumes. I only found a correlation around 75%. When I adjust both of these measures for TBV (Total Brain Volume, covariate method) and proceed to testing if there are sex effects in total cerebellar grey matter using linear regression, my results show that cerebellar volume is much larger in females than males when using the sum of the available FAST grey matter cerebellar volumes, and when I use the sum of the cerebellar cortex volumes provided by ASEG it appears that males have a much larger cerebellar cortex than females. Any thoughts as to why there is such a big discrepancy between segmentations ? Kind regards, Camille Williams PhD Candidate Laboratoire de Sciences Cognitives et Psycholinguistique (LSCP) Département d’Études en Sciences Cognitives École Normale Supérieure, Paris, France

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Error in mris_compute_lgi
by 肖伏龙 01 May '20

01 May '20

External Email - Use Caution hi all When I used the command "mris_compute_lgi --i lh.pial", there is an error which shows as followings: so how to solve this problem? Thank you very much!

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Ubuntu VM password
by Alex Mihai 01 May '20

01 May '20

External Email - Use Caution Hi guys! I have followed the virtual machine setup for virtual box freesurfer installation.but it ask me the password for the developer account. Which is the password? Cheers, Alex

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trac-all -bedp error
by Zeng, Qi 30 Apr '20

30 Apr '20

External Email - Use Caution Hi, I run trac-all, the log file has the following endings. "Queuing post processing stage" or "Queuing post processing stage 59 slices processed All slices processed /hpc/packages/minerva-common/freesurfer/6.0.0/freesurfer/bin/bedpostx_mgh: line 345: kill: (100952) - No such process". However, all outputs described in FSL BedpostX are generated dmri/FA, MD, V1, V2, V3 dmri.bedpostX/merged,mean,dyads, nodif_brain_mask Should I consider them as completed and move forward with -path? Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Re: [Freesurfer] FreeSurfer 7 stable
by fsbuild 30 Apr '20

30 Apr '20

External Email - Use Caution Hello Mina, On the setup page under the CentOS7 and 8 header, https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_linux, it does mention you can use the same archive and rpm installer for both CentOS7 and CentOS8.  Or the CentOS7 binaries should be backwards compatible on CentOS8.  We should eventually have a CentOS8 installer from native builds on CentOS8. To make that more clear, I changed the chart for downloads on the page, https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads, so say “use the CentOS7” archive or RPM.  Cuda is no longer officially supported as it is a moving target w.r.t NVIDIA hardware and drivers.  Maybe some other folks on the list have suggestions for GPU's.   I know Apple no longer supports NVIDIA hardware. - R. On Apr 30, 2020, at 19:44, Mina Rizkallah <dr.minafakhry(a)live.com> wrote:        External Email - Use Caution        Greetings FreeSurfer team,I have some questions regarding the latest stable version of freesurfer;1- I am currently using Centos 8, and the Freesurfer download link for this version says centos 7 not 8.. is it compatible with centos 8?2- Is it true that CUDA is no longer available for freesurfer? is there any other option for GPU acceleration? as it was crucial for recon-all speed (got 2.7 hours/subject instead of 6 hours on version 6).best regardsMina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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longitudinal dmrirc script error with the baselist
by Zeng, Qi 30 Apr '20

30 Apr '20

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

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Freesurfer May 2020