External Email - Use Caution
Hi, I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below. My command was as follow: make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 Can you please guide me to solve this issue.
Thanks
Mudathir
########################################### #@# Making average lh.white surface --------------------- Tue Apr 6 19:23:39 JST 2021 /Applications/freesurfer/subjects/avgsubject mris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 reading vertex positions from white... --------------------------------------------------- hemi = lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = avgsubject xform = talairach.xfm ---------------------------------------------------
Is a directory Is a directory ERROR: creating directory / ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf mris_average_surface failed ERROR: make_average_surface #################################################
Do you have write permissions to
/Applications/freesurfer/subjects
Of not on a mac
On 4/6/2021 6:39 AM, バキット・ムダシル wrote:
External Email - Use CautionHi, I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below. My command was as follow: make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 Can you please guide me to solve this issue.
Thanks
Mudathir
########################################### #@# Making average lh.white surface --------------------- Tue Apr 6 19:23:39 JST 2021 /Applications/freesurfer/subjects/avgsubject mris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 reading vertex positions from white...
hemi = lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = avgsubject xform = talairach.xfm
Is a directory Is a directory ERROR: creating directory / ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf mris_average_surface failed ERROR: make_average_surface #################################################
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I Think I have a permission. I ran chmod -R u+rwX to make sure, but the error was the same. Can you confirm from below please?
\mudathirbakhit$ ls -l $FREESURFER_HOME/ total 568 drwxr-xr-x 39 mudathirbakhit admin 1248 Mar 18 20:24 6.0.0 -rwxr-xr-x 1 mudathirbakhit wheel 3240 Aug 12 2020 ASegStatsLUT.txt -rwxr-xr-x 1 mudathirbakhit wheel 47514 Aug 12 2020 DefectLUT.txt -rwxr-xr-x@ 1 mudathirbakhit wheel 89181 Aug 12 2020 FreeSurferColorLUT.txt -rwxr-xr-x 1 mudathirbakhit wheel 18152 Aug 12 2020 FreeSurferEnv.csh -rwxr-xr-x 1 mudathirbakhit wheel 18223 Aug 12 2020 FreeSurferEnv.sh drwxrwxr-x@ 3 mudathirbakhit wheel 96 Mar 16 13:11 Freeview.app drwxr-xr-x 3 mudathirbakhit wheel 96 Mar 17 10:06 Freeview_backup.app -rwxr-xr-x@ 1 mudathirbakhit wheel 28381 Aug 12 2020 SegmentNoLUT.txt -rwxr-xr-x 1 mudathirbakhit wheel 1358 Aug 12 2020 SetUpFreeSurfer.csh -rwxr-xr-x 1 mudathirbakhit wheel 1350 Aug 12 2020 SetUpFreeSurfer.sh -rwxr-xr-x@ 1 mudathirbakhit wheel 4104 Aug 12 2020 Simple_surface_labels2009.txt -rwxr-xr-x 1 mudathirbakhit wheel 25476 Aug 12 2020 WMParcStatsLUT.txt -rw-r--r--@ 1 mudathirbakhit staff 2718 Apr 1 14:13 aparc+aseg.txt drwxr-xr-x 126 mudathirbakhit wheel 4032 Apr 7 07:22 average drwxr-xr-x 766 mudathirbakhit wheel 24512 Mar 17 10:06 bin -rwxr-xr-x 1 mudathirbakhit wheel 47 Aug 12 2020 build-stamp.txt drwxr-xr-x 3 mudathirbakhit wheel 96 Mar 17 19:35 color drwxr-xr-x 3 mudathirbakhit wheel 96 Aug 12 2020 diffusion drwxr-xr-x 37 mudathirbakhit wheel 1184 Aug 12 2020 docs drwxr-xr-x 3 mudathirbakhit wheel 96 Aug 12 2020 etc drwxr-xr-x 5 mudathirbakhit wheel 160 Aug 12 2020 fsafd drwxr-xr-x 6 mudathirbakhit wheel 192 Apr 7 07:22 fsfast drwxr-xr-x 6 mudathirbakhit wheel 192 Apr 7 07:22 lib -rw-r--r--@ 1 mudathirbakhit wheel 55 Feb 17 09:40 license.txt drwxr-xr-x 185 mudathirbakhit wheel 5920 Apr 7 07:22 matlab drwxr-xr-x 11 mudathirbakhit wheel 352 Apr 7 07:22 mni -rw-r--r--@ 1 mudathirbakhit staff 641 Apr 6 16:13 par.txt drwxr-xr-x 8 mudathirbakhit wheel 256 Apr 7 07:22 python drwxr-xr-x 3 mudathirbakhit wheel 96 Aug 12 2020 sessions -rwxr-xr-x 1 mudathirbakhit wheel 134 Aug 12 2020 sources.csh -rwxr-xr-x 1 mudathirbakhit wheel 132 Aug 12 2020 sources.sh drwxr-xr-x+ 42 mudathirbakhit wheel 1344 Apr 7 09:37 subjects -rwxr-xr-x 1 mudathirbakhit wheel 1681 Aug 12 2020 tkmeditParcColorsCMA drwxr-xr-x 38 mudathirbakhit wheel 1216 Apr 7 07:22 trctrain -rwxr-xr-x 1 mudathirbakhit wheel 972 Aug 12 2020 uninstall.sh
On Apr 6, 2021, at 22:30, Douglas N. Greve dgreve@MGH.HARVARD.EDU wrote:
Do you have write permissions to
/Applications/freesurfer/subjects
Of not on a mac
On 4/6/2021 6:39 AM, バキット・ムダシル wrote:
External Email - Use CautionHi, I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below. My command was as follow: make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 Can you please guide me to solve this issue.
Thanks
Mudathir
########################################### #@# Making average lh.white surface --------------------- Tue Apr 6 19:23:39 JST 2021 /Applications/freesurfer/subjects/avgsubject mris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 reading vertex positions from white...
hemi = lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = avgsubject xform = talairach.xfm
Is a directory Is a directory ERROR: creating directory / ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf mris_average_surface failed ERROR: make_average_surface #################################################
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1lPFkzP98f9IpSLW7QsaKAbDvU0OG4RYB0_ocBr7zownDrS...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1lPFkzP98f9IpSLW7QsaKAbDvU0OG4RYB0_ocBr7zownDrS...
It looks like you do there, but downstream you might not. In general, macs don't like to give you permission in the apps folder. Try pointer your SUBJECTS_DIR to another location, eg, in your home directory
On 4/6/2021 8:44 PM, バキット・ムダシル wrote:
External Email - Use Caution
I Think I have a permission. I ran chmod -R u+rwX to make sure, but the error was the same. Can you confirm from below please?
\mudathirbakhit$ ls -l $FREESURFER_HOME/ total 568 drwxr-xr-x 39 mudathirbakhit admin 1248 Mar 18 20:24 6.0.0 -rwxr-xr-x 1 mudathirbakhit wheel 3240 Aug 12 2020 ASegStatsLUT.txt -rwxr-xr-x 1 mudathirbakhit wheel 47514 Aug 12 2020 DefectLUT.txt -rwxr-xr-x@ 1 mudathirbakhit wheel 89181 Aug 12 2020 FreeSurferColorLUT.txt -rwxr-xr-x 1 mudathirbakhit wheel 18152 Aug 12 2020 FreeSurferEnv.csh -rwxr-xr-x 1 mudathirbakhit wheel 18223 Aug 12 2020 FreeSurferEnv.sh drwxrwxr-x@ 3 mudathirbakhit wheel 96 Mar 16 13:11 Freeview.app drwxr-xr-x 3 mudathirbakhit wheel 96 Mar 17 10:06 Freeview_backup.app -rwxr-xr-x@ 1 mudathirbakhit wheel 28381 Aug 12 2020 SegmentNoLUT.txt -rwxr-xr-x 1 mudathirbakhit wheel 1358 Aug 12 2020 SetUpFreeSurfer.csh -rwxr-xr-x 1 mudathirbakhit wheel 1350 Aug 12 2020 SetUpFreeSurfer.sh -rwxr-xr-x@ 1 mudathirbakhit wheel 4104 Aug 12 2020 Simple_surface_labels2009.txt -rwxr-xr-x 1 mudathirbakhit wheel 25476 Aug 12 2020 WMParcStatsLUT.txt -rw-r--r--@ 1 mudathirbakhit staff 2718 Apr 1 14:13 aparc+aseg.txt drwxr-xr-x 126 mudathirbakhit wheel 4032 Apr 7 07:22 average drwxr-xr-x 766 mudathirbakhit wheel 24512 Mar 17 10:06 bin -rwxr-xr-x 1 mudathirbakhit wheel 47 Aug 12 2020 build-stamp.txt drwxr-xr-x 3 mudathirbakhit wheel 96 Mar 17 19:35 color drwxr-xr-x 3 mudathirbakhit wheel 96 Aug 12 2020 diffusion drwxr-xr-x 37 mudathirbakhit wheel 1184 Aug 12 2020 docs drwxr-xr-x 3 mudathirbakhit wheel 96 Aug 12 2020 etc drwxr-xr-x 5 mudathirbakhit wheel 160 Aug 12 2020 fsafd drwxr-xr-x 6 mudathirbakhit wheel 192 Apr 7 07:22 fsfast drwxr-xr-x 6 mudathirbakhit wheel 192 Apr 7 07:22 lib -rw-r--r--@ 1 mudathirbakhit wheel 55 Feb 17 09:40 license.txt drwxr-xr-x 185 mudathirbakhit wheel 5920 Apr 7 07:22 matlab drwxr-xr-x 11 mudathirbakhit wheel 352 Apr 7 07:22 mni -rw-r--r--@ 1 mudathirbakhit staff 641 Apr 6 16:13 par.txt drwxr-xr-x 8 mudathirbakhit wheel 256 Apr 7 07:22 python drwxr-xr-x 3 mudathirbakhit wheel 96 Aug 12 2020 sessions -rwxr-xr-x 1 mudathirbakhit wheel 134 Aug 12 2020 sources.csh -rwxr-xr-x 1 mudathirbakhit wheel 132 Aug 12 2020 sources.sh drwxr-xr-x+ 42 mudathirbakhit wheel 1344 Apr 7 09:37 subjects -rwxr-xr-x 1 mudathirbakhit wheel 1681 Aug 12 2020 tkmeditParcColorsCMA drwxr-xr-x 38 mudathirbakhit wheel 1216 Apr 7 07:22 trctrain -rwxr-xr-x 1 mudathirbakhit wheel 972 Aug 12 2020 uninstall.sh
On Apr 6, 2021, at 22:30, Douglas N. Greve <dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU> wrote:
Do you have write permissions to
/Applications/freesurfer/subjects
Of not on a mac
On 4/6/2021 6:39 AM, バキット・ムダシル wrote:
External Email - Use Caution
Hi, I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below. My command was as follow: make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 Can you please guide me to solve this issue.
Thanks
Mudathir
########################################### #@# Making average lh.white surface --------------------- Tue Apr 6 19:23:39 JST 2021 /Applications/freesurfer/subjects/avgsubject mris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 reading vertex positions from white...
hemi = lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = avgsubject xform = talairach.xfm
Is a directory Is a directory ERROR: creating directory / ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf mris_average_surface failed ERROR: make_average_surface #################################################
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks Douglas. Here what happened. I did as you said and moved the $SUBJECTS_DIR out of the /Applications folder to somewhere in my home folder. Still the same error. But when I did ran the command through freesurfer 6 it worked fine even in the /Applications folder. Also, a freesurfer 7 in an Ubuntu virtual machine worked fine. So I think it has to do with something in the freesurfer 7.1.1 version I have in my computer.
I would like to add a question if you don’t mind. Since I found here in the forum that the average is in the MNI305 space, how I can make an average of my sample in MNI152 space from the start?
Thanks
Mudathir
On Apr 14, 2021, at 23:26, Douglas N. Greve dgreve@MGH.HARVARD.EDU wrote:
It looks like you do there, but downstream you might not. In general, macs don't like to give you permission in the apps folder. Try pointer your SUBJECTS_DIR to another location, eg, in your home directory
On 4/6/2021 8:44 PM, バキット・ムダシル wrote:
External Email - Use CautionI Think I have a permission. I ran chmod -R u+rwX to make sure, but the error was the same. Can you confirm from below please?
\mudathirbakhit$ ls -l $FREESURFER_HOME/ total 568 drwxr-xr-x 39 mudathirbakhit admin 1248 Mar 18 20:24 6.0.0 -rwxr-xr-x 1 mudathirbakhit wheel 3240 Aug 12 2020 ASegStatsLUT.txt -rwxr-xr-x 1 mudathirbakhit wheel 47514 Aug 12 2020 DefectLUT.txt -rwxr-xr-x@ 1 mudathirbakhit wheel 89181 Aug 12 2020 FreeSurferColorLUT.txt -rwxr-xr-x 1 mudathirbakhit wheel 18152 Aug 12 2020 FreeSurferEnv.csh -rwxr-xr-x 1 mudathirbakhit wheel 18223 Aug 12 2020 FreeSurferEnv.sh drwxrwxr-x@ 3 mudathirbakhit wheel 96 Mar 16 13:11 Freeview.app drwxr-xr-x 3 mudathirbakhit wheel 96 Mar 17 10:06 Freeview_backup.app -rwxr-xr-x@ 1 mudathirbakhit wheel 28381 Aug 12 2020 SegmentNoLUT.txt -rwxr-xr-x 1 mudathirbakhit wheel 1358 Aug 12 2020 SetUpFreeSurfer.csh -rwxr-xr-x 1 mudathirbakhit wheel 1350 Aug 12 2020 SetUpFreeSurfer.sh -rwxr-xr-x@ 1 mudathirbakhit wheel 4104 Aug 12 2020 Simple_surface_labels2009.txt -rwxr-xr-x 1 mudathirbakhit wheel 25476 Aug 12 2020 WMParcStatsLUT.txt -rw-r--r--@ 1 mudathirbakhit staff 2718 Apr 1 14:13 aparc+aseg.txt drwxr-xr-x 126 mudathirbakhit wheel 4032 Apr 7 07:22 average drwxr-xr-x 766 mudathirbakhit wheel 24512 Mar 17 10:06 bin -rwxr-xr-x 1 mudathirbakhit wheel 47 Aug 12 2020 build-stamp.txt drwxr-xr-x 3 mudathirbakhit wheel 96 Mar 17 19:35 color drwxr-xr-x 3 mudathirbakhit wheel 96 Aug 12 2020 diffusion drwxr-xr-x 37 mudathirbakhit wheel 1184 Aug 12 2020 docs drwxr-xr-x 3 mudathirbakhit wheel 96 Aug 12 2020 etc drwxr-xr-x 5 mudathirbakhit wheel 160 Aug 12 2020 fsafd drwxr-xr-x 6 mudathirbakhit wheel 192 Apr 7 07:22 fsfast drwxr-xr-x 6 mudathirbakhit wheel 192 Apr 7 07:22 lib -rw-r--r--@ 1 mudathirbakhit wheel 55 Feb 17 09:40 license.txt drwxr-xr-x 185 mudathirbakhit wheel 5920 Apr 7 07:22 matlab drwxr-xr-x 11 mudathirbakhit wheel 352 Apr 7 07:22 mni -rw-r--r--@ 1 mudathirbakhit staff 641 Apr 6 16:13 par.txt drwxr-xr-x 8 mudathirbakhit wheel 256 Apr 7 07:22 python drwxr-xr-x 3 mudathirbakhit wheel 96 Aug 12 2020 sessions -rwxr-xr-x 1 mudathirbakhit wheel 134 Aug 12 2020 sources.csh -rwxr-xr-x 1 mudathirbakhit wheel 132 Aug 12 2020 sources.sh drwxr-xr-x+ 42 mudathirbakhit wheel 1344 Apr 7 09:37 subjects -rwxr-xr-x 1 mudathirbakhit wheel 1681 Aug 12 2020 tkmeditParcColorsCMA drwxr-xr-x 38 mudathirbakhit wheel 1216 Apr 7 07:22 trctrain -rwxr-xr-x 1 mudathirbakhit wheel 972 Aug 12 2020 uninstall.sh
On Apr 6, 2021, at 22:30, Douglas N. Greve <dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU> wrote:
Do you have write permissions to
/Applications/freesurfer/subjects
Of not on a mac
On 4/6/2021 6:39 AM, バキット・ムダシル wrote:
External Email - Use CautionHi, I am trying to make an average subject but when the process reaches mris_average_surface it fails as seen below. My command was as follow: make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 Can you please guide me to solve this issue.
Thanks
Mudathir
########################################### #@# Making average lh.white surface --------------------- Tue Apr 6 19:23:39 JST 2021 /Applications/freesurfer/subjects/avgsubject mris_make_average_surface -i 7 -o white -sdir-out /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10 reading vertex positions from white...
hemi = lh avg_surf_name = white canon_surf_name = sphere.reg out_sname = avgsubject xform = talairach.xfm
Is a directory Is a directory ERROR: creating directory / ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf mris_average_surface failed ERROR: make_average_surface #################################################
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/13wllHzkvwns0NAE11TSnoi-txB2m8FE-YRCybcEIGL_tAY... https://secure-web.cisco.com/13wllHzkvwns0NAE11TSnoi-txB2m8FE-YRCybcEIGL_tAY_I42TUGXuuThLfuJQLHh48hS34wNMjx3SMtmjEWSqfUSLxUHVW9OfXN23gibofpGvtiUEdRinywLRlTheVkgVPI7EWgFwePCJ8JpwwCh8FHhryX0BAGkrHEZkzYhY_l5GOsG83kXAexQ_r2TZkCA2EPJ2BHRJlwYzKFrFmyCj1ik1jSAKgJmve2lDwSNTT0G68dGOyLN18ItQYHzpjwntdtHdJocHntgV_ZBuYfw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/13wllHzkvwns0NAE11TSnoi-txB2m8FE-YRCybcEIGL_tAY... https://secure-web.cisco.com/13wllHzkvwns0NAE11TSnoi-txB2m8FE-YRCybcEIGL_tAY_I42TUGXuuThLfuJQLHh48hS34wNMjx3SMtmjEWSqfUSLxUHVW9OfXN23gibofpGvtiUEdRinywLRlTheVkgVPI7EWgFwePCJ8JpwwCh8FHhryX0BAGkrHEZkzYhY_l5GOsG83kXAexQ_r2TZkCA2EPJ2BHRJlwYzKFrFmyCj1ik1jSAKgJmve2lDwSNTT0G68dGOyLN18ItQYHzpjwntdtHdJocHntgV_ZBuYfw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/13wllHzkvwns0NAE11TSnoi-txB2m8FE-YRCybcEIGL_tAY... https://secure-web.cisco.com/13wllHzkvwns0NAE11TSnoi-txB2m8FE-YRCybcEIGL_tAY_I42TUGXuuThLfuJQLHh48hS34wNMjx3SMtmjEWSqfUSLxUHVW9OfXN23gibofpGvtiUEdRinywLRlTheVkgVPI7EWgFwePCJ8JpwwCh8FHhryX0BAGkrHEZkzYhY_l5GOsG83kXAexQ_r2TZkCA2EPJ2BHRJlwYzKFrFmyCj1ik1jSAKgJmve2lDwSNTT0G68dGOyLN18ItQYHzpjwntdtHdJocHntgV_ZBuYfw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/13wllHzkvwns0NAE11TSnoi-txB2m8FE-YRCybcEIGL_tAY...
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
バキット・ムダシル