Re: [Freesurfer] mris_average_surface fails

2021-04-18 Thread fsbuild 
External Email - Use Caution

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 fooPassword:
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,https://secure-web.cisco.com/1xtJzx0lQIrKf7ZCl0ntd1jilGKonbJiHvRDb7FRZbR4FJp5DhU4Tdht4S1iAOPKKXATrwjbXI3PlGd0IVWQH3JEDXk4X_SRGJ9ofHHDRH5yhxJ8uv5Rvaynmlwi7KhaEt8Akxfc8jG3W8PYzvkVCCPLR3I8_ztXBBrwlwB8RCVPBvRzyh6CwcgXfIA9TbVR_4misXtNtC6gd18NY2RmwqQ82-Izw7bcVDV9wjS_kjTo5tW7rM6eZsSf_wNiqSJBOHexaB8rvlch_ST8ot_iH2w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.1.1%2Ffreesurfer-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/$ ( cd 
 /Applications/freesurfer/7.1.1; tar cpf - subjects) | tar xpf -
$ ls subjectsREADME*           
  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  
wrote:External Email - Use 
CautionThanks 
Douglas. Here what happened. I did as you said and moved the $SUBJECTS_DIR 
out of the /Applications folder to somewhere in my home folder. Still the same 
error. But when I did ran the command through freesurfer 6 it worked fine even 
in the /Applications folder. Also, a freesurfer 7 in an Ubuntu virtual machine 
worked fine. So I think it has to do with something in the freesurfer 7.1.1 
version I have in my computer.I would like to add a question if you don’t mind. 
Since I found here in the forum that the average is in the MNI305 space, how I 
can make an average of my sample in MNI152 space from the 
start?ThanksMudathirOn Apr 14, 2021, at 23:26, Douglas N. Greve 
 wrote:It looks like you do there, but downstream 
you might not. In general, macs don't like to give you permission in the apps 
folder. Try pointer your SUBJECTS_DIR to another location, eg, in your home 
directoryOn 4/6/2021 8:44 PM, バキット・ムダシル 
wrote:External Email - Use 
CautionI Think I have a 
permission. I ran chmod -R u+rwX to make sure, but the error was the same. Can 
you confirm from below please?\mudathirbakhit$ ls -l $FREESURFER_HOME/total 
568drwxr-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.shdrwxrwxr-x@   

Re: [Freesurfer] mris_average_surface fails

2021-04-18 Thread バキット・ムダシル 
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  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 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-x1 mudathirbakhit  wheel   3240 Aug 12  2020 ASegStatsLUT.txt
>> -rwxr-xr-x1 mudathirbakhit  wheel  47514 Aug 12  2020 DefectLUT.txt
>> -rwxr-xr-x@   1 mudathirbakhit  wheel  89181 Aug 12  2020 
>> FreeSurferColorLUT.txt
>> -rwxr-xr-x1 mudathirbakhit  wheel  18152 Aug 12  2020 FreeSurferEnv.csh
>> -rwxr-xr-x1 mudathirbakhit  wheel  18223 Aug 12  2020 FreeSurferEnv.sh
>> drwxrwxr-x@   3 mudathirbakhit  wheel 96 Mar 16 13:11 Freeview.app
>> drwxr-xr-x3 mudathirbakhit  wheel 96 Mar 17 10:06 Freeview_backup.app
>> -rwxr-xr-x@   1 mudathirbakhit  wheel  28381 Aug 12  2020 SegmentNoLUT.txt
>> -rwxr-xr-x1 mudathirbakhit  wheel   1358 Aug 12  2020 SetUpFreeSurfer.csh
>> -rwxr-xr-x1 mudathirbakhit  wheel   1350 Aug 12  2020 SetUpFreeSurfer.sh
>> -rwxr-xr-x@   1 mudathirbakhit  wheel   4104 Aug 12  2020 
>> Simple_surface_labels2009.txt
>> -rwxr-xr-x1 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-x1 mudathirbakhit  wheel 47 Aug 12  2020 build-stamp.txt
>> drwxr-xr-x3 mudathirbakhit  wheel 96 Mar 17 19:35 color
>> drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 diffusion
>> drwxr-xr-x   37 mudathirbakhit  wheel   1184 Aug 12  2020 docs
>> drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 etc
>> drwxr-xr-x5 mudathirbakhit  wheel160 Aug 12  2020 fsafd
>> drwxr-xr-x6 mudathirbakhit  wheel192 Apr  7 07:22 fsfast
>> drwxr-xr-x6 mudathirbakhit  wheel192 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  wheel352 Apr  7 07:22 mni
>> -rw-r--r--@   1 mudathirbakhit  staff641 Apr  6 16:13 par.txt
>> drwxr-xr-x8 mudathirbakhit  wheel256 Apr  7 07:22 python
>> drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 sessions
>> -rwxr-xr-x1 mudathirbakhit  wheel134 Aug 12  2020 sources.csh
>> -rwxr-xr-x1 mudathirbakhit  wheel132 Aug 12  2020 sources.sh
>> drwxr-xr-x+  42 mudathirbakhit  wheel   1344 Apr  7 09:37 subjects
>> -rwxr-xr-x1 mudathirbakhit  wheel   1681 Aug 12  2020 
>> tkmeditParcColorsCMA
>> drwxr-xr-x   38 mudathirbakhit  wheel   1216 Apr  7 07:22 trctrain
>> -rwxr-xr-x1 mudathirbakhit  wheel972 Aug 12  2020 uninstall.sh
>> 
>>> On Apr 6, 2021, at 22:30, Douglas N. Greve >> > 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
 read

Re: [Freesurfer] mris_average_surface fails

2021-04-14 Thread Douglas N. Greve 
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 > 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
#






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Freesurfer mailing list
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



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Freesurfer@nmr.mgh.harvard.edu
ht

Re: [Freesurfer] mris_average_surface fails

2021-04-06 Thread バキット・ムダシル 
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-x1 mudathirbakhit  wheel   3240 Aug 12  2020 ASegStatsLUT.txt
-rwxr-xr-x1 mudathirbakhit  wheel  47514 Aug 12  2020 DefectLUT.txt
-rwxr-xr-x@   1 mudathirbakhit  wheel  89181 Aug 12  2020 FreeSurferColorLUT.txt
-rwxr-xr-x1 mudathirbakhit  wheel  18152 Aug 12  2020 FreeSurferEnv.csh
-rwxr-xr-x1 mudathirbakhit  wheel  18223 Aug 12  2020 FreeSurferEnv.sh
drwxrwxr-x@   3 mudathirbakhit  wheel 96 Mar 16 13:11 Freeview.app
drwxr-xr-x3 mudathirbakhit  wheel 96 Mar 17 10:06 Freeview_backup.app
-rwxr-xr-x@   1 mudathirbakhit  wheel  28381 Aug 12  2020 SegmentNoLUT.txt
-rwxr-xr-x1 mudathirbakhit  wheel   1358 Aug 12  2020 SetUpFreeSurfer.csh
-rwxr-xr-x1 mudathirbakhit  wheel   1350 Aug 12  2020 SetUpFreeSurfer.sh
-rwxr-xr-x@   1 mudathirbakhit  wheel   4104 Aug 12  2020 
Simple_surface_labels2009.txt
-rwxr-xr-x1 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-x1 mudathirbakhit  wheel 47 Aug 12  2020 build-stamp.txt
drwxr-xr-x3 mudathirbakhit  wheel 96 Mar 17 19:35 color
drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 diffusion
drwxr-xr-x   37 mudathirbakhit  wheel   1184 Aug 12  2020 docs
drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 etc
drwxr-xr-x5 mudathirbakhit  wheel160 Aug 12  2020 fsafd
drwxr-xr-x6 mudathirbakhit  wheel192 Apr  7 07:22 fsfast
drwxr-xr-x6 mudathirbakhit  wheel192 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  wheel352 Apr  7 07:22 mni
-rw-r--r--@   1 mudathirbakhit  staff641 Apr  6 16:13 par.txt
drwxr-xr-x8 mudathirbakhit  wheel256 Apr  7 07:22 python
drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 sessions
-rwxr-xr-x1 mudathirbakhit  wheel134 Aug 12  2020 sources.csh
-rwxr-xr-x1 mudathirbakhit  wheel132 Aug 12  2020 sources.sh
drwxr-xr-x+  42 mudathirbakhit  wheel   1344 Apr  7 09:37 subjects
-rwxr-xr-x1 mudathirbakhit  wheel   1681 Aug 12  2020 tkmeditParcColorsCMA
drwxr-xr-x   38 mudathirbakhit  wheel   1216 Apr  7 07:22 trctrain
-rwxr-xr-x1 mudathirbakhit  wheel972 Aug 12  2020 uninstall.sh

> On Apr 6, 2021, at 22:30, Douglas N. Greve  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
>> https://secure-web.cisco.com/1lPFkzP98f9IpSLW7QsaKAbDvU0OG4RYB0_ocBr7zownDrSRz7-pM_qO7gblUlTW0ULzx03mvHB0nLMd-d5PVB6oLx4bzelxvSAiK6jepnnMPlJLDXpPLXDrS0sO4uCr2mqArn7KcBrGczCFnTz2ZH7GH5ISGXxA64sBCRhG58H6ZgZYpquKXAHgj4oMQ3dK1lSdB-Pyzz9159CzM7LC4-dFdNwnpj0U1GKcRVqqN7x8lVCZ3bS2MvXHJGfTcNq0V5Hf3EziNNdibNSclvJX5MA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1lPFkzP98f9IpSLW7QsaKA

Re: [Freesurfer] mris_average_surface fails

2021-04-06 Thread Douglas N. Greve 
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
> #
>
>
>
>
>
>
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[Freesurfer] mris_average_surface fails

2021-04-06 Thread バキット・ムダシル 
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
#






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