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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:

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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:
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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
#################################################






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