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Hello Mudathir,

Your account needs admin/sudo privileges in order to write files under /Applications.  If you made the first account on the machine when it was new and powered up after taking it out of the box, then at the terminal all you should need to do is preface commands with “sudo”.  If you use the Finder, then it will ask you to authenticate via a popup window, e.g., when installing software.  Once you authenticate via the terminal or via the Finder window and the system accepts your password, then by default your admin permissions will be cached for a certain period of time.

One way to test that is to open a terminal window and do,

$ sudo touch /Applications foo
<output deleted>
Password:

If that succeeds, then you should be able to remove the file w/o typing sudo while your credentials are still cached,
$ rm /Applications/foo

With admin/sudo privileges, the 7.1.1 Mac package installer program,
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-darwin-macOS-7.1.1.pkg

- can be used to install the freesurfer 7.1.1 distribution under /Applications/freesurfer/7.1.1.  The freesurfer 6 or freesurfer 7 *.pkg files should set all the permissions to be correct on the freesurfer files.

You can re-home SUBJECTS_DIR in the shell environment (this example assumes the pkg file installed it as /Applications/freesurfer/7.1.1)

$ bash
$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

-------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.1.1
FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/7..1.1/subjects
MNI_DIR           /Applications/freesurfer/7.1.1/mni

You can change the setting of SUBJECTS_DIR to point to a directory where you always have write permission (do not need to authenticate with sudo), e.g., your home directory,

$ mkdir $HOME/subjects
$ export SUBJECTS_DIR=$HOME/subjects

If you have at least ~3G of free space, you could just copy the contents of the ./subjects dir from the freesurfer distribution into $HOME/subjects,

$ cd $HOME
$ pwd
/Users/<username>
$ ( cd  /Applications/freesurfer/7.1.1; tar cpf - subjects) | tar xpf -

$ ls subjects
README*             cvs_avg35/          fsaverage3/         fsaverage6/         rh.EC_average/
V1_average/         cvs_avg35_inMNI152/ fsaverage4/         fsaverage_sym/      sample-001.mgz*
bert/               fsaverage/          fsaverage5/         lh.EC_average/      sample-002.mgz*

You can always start again from scratch after processing files by removing ./subejcts under your $HOME directory and copy the files over again via the tar command (w/o touching the installed freesurfer distribution).

- R.


On Apr 18, 2021, at 04:41, バキット・ムダシル <m-bakhit@fmu.ac.jp> wrote:

        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:

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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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