Re: [Freesurfer] freesurfer running error at start

[fsbuild]

External Email - Use Caution

Your output shows you should you should be ready to work with freesurfer 
version 6.0 which is an older release from ~2017.  So people there may 
have used version 6 for quite some time.   If there was something missing 
on the system that freesurfer 6 needed to run, it’s probably been remedied by 
now.  If you are just starting out with freesurfer then I would not be too 
concerned with using version 6.
Just keep in mind the current release is version 7.2.0 from this year (2021). 
 Browsing the 7.X release notes (at the top of the page) and comparing 
then with the 6.0 release notes (at the bottom of the page) can help you decide 
if version 7 offers improvements depending upon what you need to do - see 
 https://secure-web.cisco.com/1BDXGUYepZSu-OnlNwiqwjMw9yYjoVH9lFYYgCyki-ZNot8TkGmaIVwTD9K5BQZzvk4HPvMrJ70VW_4L4LS4YCgONmrFbWrWSrr1SNqCc5eBh9Dkgm6gXT5a6iILq6cs4QyT0bhqBlK3UNMV7iayEbLgUxXWayiDLf0uImbHIg44Fs9ZY3h23oKWKU68tDgSkNZQiHtSz7k_uP8qWWVg3p1hRr3Sl0vZBeZEb3O6d3rEVs_ugFAfUBbbHaE6ey9MK2zgpKB3RxWjRpsiRBloIdQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes.
  For ongoing work it’s recommended to stick with the version of 
freesurfer you started with  -  see the “Important Note” on this 
page, https://secure-web.cisco.com/1PMV3hWYoa71yGCIFhXRqSneCKhKc1Kl4cvy0kySa6-DoulML5AYQbAMMssfOE9Q4293pssdVAEVN6gN30OYcmajuSW_FAuZQinx7bmsPHAL7t7-nZ0GfWhh6bVmPvX5FYQ1VKMQO-qph0HnXIRWoNYq7GV6tvD-sX7VIM2oINMCgghUUGfBJ9xOSNLafQxfsYSYYfXDGjHqZNOl-YzPyVfnfihy8tSeIUyn9KmxKULUzOlIIoRnAZPwCGxeAWHdqMV_vy-jn6WUwaPlr8EYPUQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FDownloadAndInstall.
- R.
On Sep 23, 2021, at 18:25, Banik, Rana  
wrote:External Email - Use 
CautionExternal
 Email - Use 
Cautionbanikr2@banikr:~$ 
bashbanikr2@banikr:~$ export 
FREESURFER_HOME=/usr/local/freesurferbanikr2@banikr:~$ source 
SFREESURFER_HOME/SetUpFreeSurfer.shbash: SFREESURFER_HOME/SetUpFreeSurfer.sh: 
No such file or directoryInstead, I changed the command 
as: banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.shgives 
the following: banikr2@banikr:~$ source 
/usr/local/freesurfer/SetUpFreeSurfer.sh 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Setting up 
environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   
/usr/local/freesurferFSFAST_HOME       
/usr/local/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR     
 /usr/local/freesurfer/subjectsMNI_DIR           
/usr/local/freesurfer/mniFSL_DIR           
/usr/local/fslHow do I check the installation is done properly? FYI, I 
have used mri_convert from python script.Rana BanikFrom: fsbuild 
Sent: Thursday, September 23, 2021 4:11 
PMTo: freesurfer@nmr.mgh.harvard.edu Cc: Banik,
 Rana Subject: Re: [Freesurfer] 
freesurfer running error at start OK, then try setting FREESURFER_HOME and 
setting the environment in a terminal window with the commands,$ bash$ export 
FREESURFER_HOME=/usr/local/freesurfer$ source 
$FREESURFER_HOME/SetUpFreeSurfer.shThen you should see what the output reports 
for the freesurfer version.- R.On Sep 23, 2021, at 15:30, Banik, Rana 
 
wrote:External Email - Use 
CautionExternal
 Email - Use 
CautionHello, There is no 
directory called /7.2.0 rather the directory i am finding the files 
is: 
banikr2@banikr:/usr/local/freesurfer$ 
pwd/usr/local/freesurfer
Trying the same in the /freesurfer 
folderRana BanikFrom: fsbuild 
Sent: Wednesday, September 22, 2021 7:11 
PMTo: freesurfer@nmr.mgh.harvard.edu Cc: Banik,
 Rana Subject: Re: [Freesurfer] 
freesurfer running error at start Hello Rana,Running that script (or any 
other freesurfer commands/binaries) assumes you’ve setup the freesurfer 
environment by,1) setting FREESURFER_HOME in your shell to point to the top of 
the freesurfer tree2) source’ing a shell init file to set PATH and other 
environment variables in order to run freesurfer commandsThere is info on the 
wiki about this for linux,MailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux- and the 
Mac,MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_MacJust find the 
absolute path to the top of the freesurfer tree.  For the latest 7.2.0 
release installed by the package installers the version number is already in 
the absolute pathname to the top of the freesurfer tree.  On linux that 
path would be /usr/local/freesurfer/7.2.0 and on the Mac that path would be 
/Applications/freesurfer/7.2.

Re: [Freesurfer] Customising overlay

[Worker, Amanda]

External Email - Use Caution

Hi,

I was using version 6.0.0 but I have just tried 7.1.1 and it works fine. Thank 
you!

Amanda

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wang, Ruopeng 

Sent: 23 September 2021 16:56
To: Freesurfer support list 
Subject: Re: [Freesurfer] Customising overlay

You don't often get email from rwa...@mgh.harvard.edu. Learn why this is 
important
What version of freesurfer are you using? I tried the latest freeview build and 
had no problem inserting colors at arbitrary value for customized color option.

Best,
Ruopeng


On Sep 23, 2021, at 9:00 AM, Worker, Amanda 
mailto:amanda.wor...@kcl.ac.uk>> wrote:

External Email - Use Caution

External Email - Use Caution

Dear FreeSurfer Developers,

I am attempting to create some figures which display regional (Destrieux atlas) 
values which are typically in the range of 0-10. I would like to have an 
inflated brain with those regional values overlaid, for both patients and 
healthy controls. In total there will be four independent figures. The problem 
I am having is that the range of values is different for each overlay e.g. 
overlay 1 regional value range from 0-3, overlay 2 regional values range from 
0-8, which means that the colour scales are on different scales. I would like 
to find a way to manually set the scale to 0-10 for each overlay, regardless of 
the actual values that exist within the overlay file.

I am currently using the below command to load the overlay and then manually 
configuring the colour scale via the custom option, but I cannot add a point 
that is outside the range of values that exist in that overlay. I hope this 
makes sense and I would appreciate any advice you can give on how to achieve 
consistent colour scales for different overlays.

freeview -f 
/software/system/freesurfer/freesurfer-6.0.0/subjects/fsaverage/surf/rh.inflated:overlay=rh_pcnt_neg_control_01.mgz:overlay_method=linearopaque:overlay_threshold=0,5,10

Kind regards,

Amanda
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] freesurfer running error at start

[Banik, Rana]

External Email - Use Caution

additionally, running freeview gives me the following error:

banikr2@banikr:~$ freeview
freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open 
shared object file: No such file or directory

Then I tried to install libpng12.so.0 with sudo but got more errors:

banikr2@banikr:~$ sudo apt-get install libpng12.so.0
[sudo] password for banikr2:
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package libpng12.so.0
E: Couldn't find any package by glob 'libpng12.so.0'
E: Couldn't find any package by regex 'libpng12.so.0'

Rana


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Banik, Rana 

Sent: Thursday, September 23, 2021 5:25 PM
To: fsbuild ; freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] freesurfer running error at start


External Email - Use Caution

banikr2@banikr:~$ bash
banikr2@banikr:~$ export FREESURFER_HOME=/usr/local/freesurfer
banikr2@banikr:~$ source SFREESURFER_HOME/SetUpFreeSurfer.sh

bash: SFREESURFER_HOME/SetUpFreeSurfer.sh: No such file or directory

Instead, I changed the command as:
banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.sh

gives the following:
banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.sh
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl

How do I check the installation is done properly?
FYI, I have used mri_convert from python script.

Rana Banik


From: fsbuild 
Sent: Thursday, September 23, 2021 4:11 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Banik, Rana 
Subject: Re: [Freesurfer] freesurfer running error at start

OK, then try setting FREESURFER_HOME and setting the environment in a terminal 
window with the commands,

$ bash
$ export FREESURFER_HOME=/usr/local/freesurfer
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

Then you should see what the output reports for the freesurfer version.

- R.

On Sep 23, 2021, at 15:30, Banik, Rana  wrote:

External Email - Use Caution
External Email - Use Caution
Hello,

There is no directory called /7.2.0 rather the directory i am finding the files 
is:
banikr2@banikr:/usr/local/freesurfer$ pwd
/usr/local/freesurfer


Trying the same in the /freesurfer folder

Rana Banik


From: fsbuild mailto:fsbu...@contbay.com>>
Sent: Wednesday, September 22, 2021 7:11 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Banik, Rana mailto:rana.ba...@vanderbilt.edu>>
Subject: Re: [Freesurfer] freesurfer running error at start

Hello Rana,

Running that script (or any other freesurfer commands/binaries) assumes you’ve 
setup the freesurfer environment by,

1) setting FREESURFER_HOME in your shell to point to the top of the freesurfer 
tree
2) source’ing a shell init file to set PATH and other environment variables in 
order to run freesurfer commands

There is info on the wiki about this for linux,
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux

Re: [Freesurfer] freesurfer running error at start

[Banik, Rana]

External Email - Use Caution

banikr2@banikr:~$ bash
banikr2@banikr:~$ export FREESURFER_HOME=/usr/local/freesurfer
banikr2@banikr:~$ source SFREESURFER_HOME/SetUpFreeSurfer.sh

bash: SFREESURFER_HOME/SetUpFreeSurfer.sh: No such file or directory

Instead, I changed the command as:
banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.sh

gives the following:
banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.sh
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl

How do I check the installation is done properly?
FYI, I have used mri_convert from python script.

Rana Banik


From: fsbuild 
Sent: Thursday, September 23, 2021 4:11 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Banik, Rana 
Subject: Re: [Freesurfer] freesurfer running error at start

OK, then try setting FREESURFER_HOME and setting the environment in a terminal 
window with the commands,

$ bash
$ export FREESURFER_HOME=/usr/local/freesurfer
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

Then you should see what the output reports for the freesurfer version.

- R.

On Sep 23, 2021, at 15:30, Banik, Rana  wrote:

External Email - Use Caution
External Email - Use Caution
Hello,

There is no directory called /7.2.0 rather the directory i am finding the files 
is:
banikr2@banikr:/usr/local/freesurfer$ pwd
/usr/local/freesurfer


Trying the same in the /freesurfer folder

Rana Banik


From: fsbuild mailto:fsbu...@contbay.com>>
Sent: Wednesday, September 22, 2021 7:11 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Banik, Rana mailto:rana.ba...@vanderbilt.edu>>
Subject: Re: [Freesurfer] freesurfer running error at start

Hello Rana,

Running that script (or any other freesurfer commands/binaries) assumes you’ve 
setup the freesurfer environment by,

1) setting FREESURFER_HOME in your shell to point to the top of the freesurfer 
tree
2) source’ing a shell init file to set PATH and other environment variables in 
order to run freesurfer commands

There is info on the wiki about this for linux,
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux
- and the Mac,
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac

Re: [Freesurfer] freesurfer running error at start

[fsbuild]

External Email - Use Caution

OK, then try setting FREESURFER_HOME and setting the environment in a terminal 
window with the commands,
$ bash
$ export FREESURFER_HOME=/usr/local/freesurfer$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
Then you should see what the output reports for the freesurfer version.

- R.
On Sep 23, 2021, at 15:30, Banik, Rana  
wrote:External Email - Use 
CautionExternal
 Email - Use 
CautionHello, There is no 
directory called /7.2.0 rather the directory i am finding the files 
is: 
banikr2@banikr:/usr/local/freesurfer$ 
pwd/usr/local/freesurfer
Trying the same in the /freesurfer 
folderRana BanikFrom: fsbuild 
Sent: Wednesday, September 22, 2021 7:11 
PMTo: freesurfer@nmr.mgh.harvard.edu Cc: Banik,
 Rana Subject: Re: [Freesurfer] 
freesurfer running error at start Hello Rana,Running that script (or any 
other freesurfer commands/binaries) assumes you’ve setup the freesurfer 
environment by,1) setting FREESURFER_HOME in your shell to point to the top of 
the freesurfer tree2) source’ing a shell init file to set PATH and other 
environment variables in order to run freesurfer commandsThere is info on the 
wiki about this for linux,MailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux- and the 
Mac,MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_MacJust find the 
absolute path to the top of the freesurfer tree.  For the latest 7.2.0 
release installed by the package installers the version number is already in 
the absolute pathname to the top of the freesurfer tree.  On linux that 
path would be /usr/local/freesurfer/7.2.0 and on the Mac that path would be 
/Applications/freesurfer/7.2.0For that linux path using bash you would do,$ 
bash$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0$ source 
$FREESURFER_HOME/SetUpFreeSurfer.shWhen you run the source command to read the 
SetUpFreeSurfer script for the shell you are using, the version of freesurfer 
will get printed out automatically for you.Using the 7.2.0 linux release you 
would see the string between the dashes no matter what the absolute path is to 
FREESURFER_HOME on your system.tmp$ export 
FREESURFER_HOME=/usr/local/freesurfer/7.2.0tmp$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh 
freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b Setting up 
environment for FreeSurfer/FS-FAST (and 
FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME  
     /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR    
  /usr/local/freesurfer/7.2.0/subjectsMNI_DIR     
      /usr/local/freesurfer/7.2.0/mniFSL_DIR   
        /usr/pubsw/packages/fsl/current… now run any 
freesurfer commands …- ROn Sep 22, 2021, at 18:04, Banik, Rana 
 
wrote:External Email - Use 
CautionExternal
 Email - Use CautionRunning 
freesurfer from terminal with the following 
error: banikr2@banikr:~/freesurfer/bin$ ./freesurfer 

FreeSurfer is a set of tools for the analysis and visualization
of structural and functional brain imaging data. FreeSurfer
also refers to the structural imaging stream within the
FreeSurfer suite.

Users should consult the online documentation available at:

  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://secure-web.cisco.com/1BX9WO2ZIUDU9BmWuM0YkMFQ5KPQ0N_6lDMeyaiAbyQnDa-ptDA2mcQ_O9ajB_UNqiwneoMs-Rgh95PsYFuqTAWnbvjg4WUnkg5SpzyIQf6fRBRx2lGYAd2_EceLEPiZsnFQIJerF5LsyGqtRVPjZ7fznXg2MEhKJLzQgxnvGofw2_hXdsuYaDFX1WGIwktjoVK0f449AxNlWxYg8Z2LJ55DgNdaKfmbmJACtJwpmCkd6LeLLn1O2NAeX7un87eqhpeIjI5tHQzW4L20PQvOLQQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu

Alternatively, the 'recon-all' command help-text provides
adequate information to begin processing subject data, such
as the sample subject 'bert' found in the 'freesurfer/subjects'
directory.  Type 'recon-all --help' to view this help-text.

Direct comments and questions to:

  freesurfer@nmr.mgh.harvard.edu

You are running this version of FreeSurfer:

cat: /build-stamp.txt: No such file or directory
Any idea what went wrong or how to fix it? Rana BanikGraduate StudentDept. 
of Biomedical Engineering Vanderbilt University, Nashville, 
TN___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1OK46XhJ4f_3Ospz1-ee0_xWo4bRUc2OoqTABw2Ah_pe27RdS-aW_pQibZAl974Pt0PYOjUCLJT08iSBJwOy6FkDfGIKfPAZJvrEb-GG4HlOoKmGJMj2V-gnQbGbxXbtVxxpQoXTWcLQn7m7cisnAWyh_xUTKuSmFr-ecgOAENC8xA_cpcBL982rkplEg2kgVAt--kwwzQSi8ocDZ5LOJkI5ulY2HiNfAIUe8X_dvuN797OzEM5

Re: [Freesurfer] glmfit sig file all zeros

[Pedersen, Walker Scott]

Here is what I get for the mask:
__

Volume information for 
/autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz
  type: nii
dimensions: 163842 x 1 x 1
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 163842.000
   dof: 1
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =  -0., z_r =  -0., c_r = 
-68268.5000
  : x_a =  -0., y_a =   1., z_a =  -0., c_a =   -17.
  : x_s =   0., y_s =   0., z_s =   1., c_s =16.5000
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -1.  -0.  -0. 13652.5000
   -0.   1.  -0.   -17.5000
0.   0.   1.16.
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0. 13652.5000
   -0.   1.  -0.17.5000
   -0.  -0.   1.   -16.
   -0.  -0.  -0. 1.

__

And here is what I get for the input ces file:
__

Volume information for 
/autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz
  type: nii
dimensions: 163842 x 1 x 1 x 17
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 163842.000
   dof: 1
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
TR: 2560.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 17
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
-68267.5000
  : x_a =   0., y_a =   0., z_a =   1., c_a =-2.5000
  : x_s =   0., y_s =  -1., z_s =   0., c_s = 0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0. 13653.5000
0.   0.   1.-3.
0.  -1.   0. 0.5000
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0. 13653.5000
   -0.  -0.  -1. 0.5000
   -0.   1.  -0. 3.
   -0.  -0.  -0. 1.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, September 23, 2021 10:19 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] glmfit sig file all zeros

It looks like the mask is the wrong size. What is the dimension of
/autofs/cluster/neuromod/NIFTI/OCD_N 
M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz
you can check with mri_info


On 9/17/2021 8:32 PM, Pedersen, Walker Scott wrote:
Hi,

I am running glmfit on some functional data (using ces.nii.gz surface files as 
input) using ROIs and the --mask argument, that I plan to later submit to 
glmfit-sim for small volume correction.  I have some rois that are subcortical 
and some that are surfaces.  For the glmfit run within the surface ROIs the 
output sig.nii.gz files all voxels have a value of zero. However, this is not 
the case for the F.nii.gz and z.nii.gz files output by the same glmfit command 
- they have non-zero voxels. This issue only occurs for the surface ROIs, when 
I run glmfit in subcortical ROIs the sig.nii.gz files look normal.

The surface ROIs were created by using afnis 3dundump to create 10mm spheres 
from MNI coordinates. I then ran the MNI template through freesurfer, and used 
the regheader from this to run mri_vol2surf to put the spherical ROIs into 
fsaverage space.  I am able to view the resulting surface ROIs projected onto 
the fsaverage surface in freeview, and have checked that my ces.nii.gz function 
files can also be overlayed onto the same fsaverage template in freeview.

The output of one of the glmfit commands in question is below.

thanks!



WARNING: gdfReadV1: no variables on 'Variables' line found
Reading source surface 
/autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/subjects/fsaverage/surf/lh.white
gdfRead(): reading 
/autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles/
/fsgd.txt
INFO: gd2mtx_method is dods
Number of 

Re: [Freesurfer] freesurfer running error at start

[Banik, Rana]

External Email - Use Caution

Hello,

There is no directory called /7.2.0 rather the directory i am finding the files 
is:
banikr2@banikr:/usr/local/freesurfer$ pwd
/usr/local/freesurfer


Trying the same in the /freesurfer folder

Rana Banik


From: fsbuild 
Sent: Wednesday, September 22, 2021 7:11 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Banik, Rana 
Subject: Re: [Freesurfer] freesurfer running error at start

Hello Rana,

Running that script (or any other freesurfer commands/binaries) assumes you’ve 
setup the freesurfer environment by,

1) setting FREESURFER_HOME in your shell to point to the top of the freesurfer 
tree
2) source’ing a shell init file to set PATH and other environment variables in 
order to run freesurfer commands

There is info on the wiki about this for linux,
https://secure-web.cisco.com/1vHW00PQkxBC5peROUD05iip8Q_yYT9RRaoKRmX0ZrL9gZgMLovqAHMW3Oq2tAy6kowtFmKrdVzfJU1NhFu_aVPSu1t4oTs5RK6FDHPolVtEAsKQNpmBBsTn4OMQLRGlJhxgmA2smPuWsxLS99DsCNKgvIKU9IiyEAhotGVkRWkdWJJqTxWkT3V3JaqylPxO1-xx1JTqFAVBJ3VPJNIOKHw-KwgkbJtKusnYT2rkLaID2PYI5ihx9k9qJvlxD-0umcr7Rf387jdMP4yTE7v2nOg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Linux
- and the Mac,
https://secure-web.cisco.com/13L-zHKeE_gApGIHzjfFCYR6tVGK5IdFjgvhmQFAnCZrUS0mhRCkUGhL67ISnWBILmb41XOr9SCR4RCaxK4lIcZLThiu8vAUKVApuXIYs7wiQqqBD-c9ekb8UL_9bXa6HZn6R4zJ7CW40PbZRlpo4eBeDLT5y3vgQIWD4zndrJ_yk1mPaqeq0R0-ef8SI8uBuRasIxIAF4hUYoKlsZ8MLkdcrlTBxfwoaLxJ6ClREmuQXRTvHpuTYIJNnwi-1G-DaDHuJxpo7eGNquQwI0k5ZEQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Mac

Just find the absolute path to the top of the freesurfer tree.  For the latest 
7.2.0 release installed by the package installers the version number is already 
in the absolute pathname to the top of the freesurfer tree.  On linux that path 
would be /usr/local/freesurfer/7.2.0 and on the Mac that path would be 
/Applications/freesurfer/7.2.0

For that linux path using bash you would do,
$ bash
$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

When you run the source command to read the SetUpFreeSurfer script for the 
shell you are using, the version of freesurfer will get printed out 
automatically for you.

Using the 7.2.0 linux release you would see the string between the dashes no 
matter what the absolute path is to FREESURFER_HOME on your system.

tmp$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0
tmp$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.2.0
FSFAST_HOME   /usr/local/freesurfer/7.2.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/7.2.0/subjects
MNI_DIR   /usr/local/freesurfer/7.2.0/mni
FSL_DIR   /usr/pubsw/packages/fsl/current

… now run any freesurfer commands …

- R

On Sep 22, 2021, at 18:04, Banik, Rana  wrote:

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Running freesurfer from terminal with the following error:


banikr2@banikr:~/freesurfer/bin$ ./freesurfer

FreeSurfer is a set of tools for the analysis and visualization
of structural and functional brain imaging data. FreeSurfer
also refers to the structur

[Freesurfer] fsaverage nifti to gifti

[Tom Vanasse]

External Email - Use Caution

Hello,

I have a question regarding the conversion of functional fsaverage lh and
rh files (created from the Yeo lab MNI to fsaverage projection software:
https://secure-web.cisco.com/1nRJbdVDTJHwxxGMU9q1fmvcPt_Df0AIfr6uIaGGD96UkPwARZlPIxtczdIoGt6VZEzwsCe1WmzWCzwArCMnu9gNDmM8U_9motL4XbyPSi6Jr7a_ixjuuKTXBvoeXldopRVeL2WinQRrLabJX_W41DX2IRwdckicxNpfe11a5J_SSAQuOSPnOxcoi2KQ3DojFD9CwKPyKu3tfpMHLOPgH1stdFqkx2TFY8b1T-tNoyQjc6Fys_J7rqL5WAo3BpVYR01SOWKSm_qR__enaletbmQ/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fregistration%2FWu2017_RegistrationFusion%2Fbin)
to a *gifti file*.

For example,
'rh.sub-13_ses-fmri1_task-awak_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold_cleaned.allSub_RF_ANTs_MNI152_orig_to_fsaverage.nii.gz'

This is necessary because my end goal is to then transform that gifti file,
using wb_command, to the fs_LR HCP surface.

Any help would be greatly appreciated,

Tom
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Re: [Freesurfer] glmfit sig file all zeros

[Douglas N. Greve]

It looks like the mask is the wrong size. What is the dimension of
/autofs/cluster/neuromod/NIFTI/OCD_N 
M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz

you can check with mri_info


On 9/17/2021 8:32 PM, Pedersen, Walker Scott wrote:

Hi,

I am running glmfit on some functional data (using ces.nii.gz surface 
files as input) using ROIs and the --mask argument, that I plan to 
later submit to glmfit-sim for small volume correction.  I have some 
rois that are subcortical and some that are surfaces.  For the glmfit 
run within the surface ROIs the output sig.nii.gz files all voxels 
have a value of zero. However, this is not the case for the F.nii.gz 
and z.nii.gz files output by the same glmfit command - they have 
non-zero voxels. This issue only occurs for the surface ROIs, when I 
run glmfit in subcortical ROIs the sig.nii.gz files look normal.


The surface ROIs were created by using afnis 3dundump to create 10mm 
spheres from MNI coordinates. I then ran the MNI template through 
freesurfer, and used the regheader from this to run mri_vol2surf to 
put the spherical ROIs into fsaverage space.  I am able to view the 
resulting surface ROIs projected onto the fsaverage surface in 
freeview, and have checked that my ces.nii.gz function files can also 
be overlayed onto the same fsaverage template in freeview.


The output of one of the glmfit commands in question is below.

thanks!



WARNING: gdfReadV1: no variables on 'Variables' line found
Reading source surface 
/autofs/cluster/neuromod/programs/freesurfer_7.1.1/freesurfer/subjects/fsaverage/surf/lh.white
gdfRead(): reading 
/autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles/

/fsgd.txt
INFO: gd2mtx_method is dods
Number of vertices 163842
Number of faces    327680
Total area         65417.00
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       0.195472

7.1.1
cwd /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast
cmdline mri_glmfit --glmdir 
/autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lC
S+E_m_lCS-atCS+E/outputFiles/lIFG/ --y 
/autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recal
l//recall.sm5.lh/lCS+E_m_lCS-atCS+E/ces.nii.gz --surf fsaverage lh 
--fsgd /autofs/space/uriline_003/users/projects/OC
D_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt --C 
/autofs/space/uriline_003/users/projects/OCD_NM/
walker_pedersen/data/image/main/recall/inputFiles//groupDiff.mtx 
--nii.gz --mask /autofs/cluster/neuromod/NIFTI/OCD_N

M/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz --eres-save
sysname  Linux
hostname r440-28.nmr.mgh.harvard.edu
machine  x86_64
user     wsp6
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y 
 /autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_lCS-atCS+E

/ces.nii.gz
logyflag 0
usedti  0
FSGD 
/autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/inputFiles//fsgd.txt
mask 
/autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/rois/recall/lIFG_surf_rad10.nii.gz

maskinv 0
glmdir 
/autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atCS+E/outp

utFiles/lIFG/
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory 
/autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+

E_m_lCS-atCS+E/outputFiles/lIFG/
Loading y from 
/autofs/cluster/neuromod/NIFTI/OCD_NM/derivatives/fsfast/concat/postMpre/recall/recall.sm5.lh/lCS+E_m_

lCS-atCS+E/ces.nii.gz
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to 
/autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_

m_lCS-atCS+E/outputFiles/lIFG//Xg.dat
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1.125
Pruning voxels by thr: 1.175494e-38
Found 512 voxels in mask
Saving mask to 
/autofs/space/uriline_003/users/projects/OCD_NM/walker_pedersen/data/image/main/recall/lCS+E_m_lCS-atC

S+E/outputFiles/lIFG//mask.nii.gz
Reshaping mriglm->mask...
search space = 222.026773
DOF = 15
Starting fit and test
Fit completed in 0.0002 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.987586, ar1std=0.043927, gstd=3.620916, fwhm=8.526606
Writing results
  groupDiff
MRImask(): AllowDiffGeom = 1
INFO: MRImask() using MRImaskDifferentGeometry()
    maxvox sig=-0  F=4.36504  at  index 391 0 0  seed=1632900996
mri_glmfit done



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Re: [Freesurfer] Announcing FreeSurfer version 7.2

[Douglas N. Greve]

On 9/23/2021 11:05 AM, Corinna Bauer wrote:


External Email - Use Caution

Hi Doug,

I'm about to start edits on subjects that have been re-processed in 
7.2 using the -fill flag. Before doing so, can you clarify/verify that 
we edit the new filled.mgz just the same as we would the wm.mgz (aside 
from the fill values being different for left vs right hemispheres)?

Correct.
I have also noticed a few spots where the filled.mgz extends beyond 
the wm surface from the wm.mgz file (see attached). Should these be 
edited to match the wm.mgz?
I'm not sure what you are pointing out. Both of those surfaces should be 
tessellated at 1mm, but I just see the white and pial.


Thanks!

Corinna

On Wed, Jul 21, 2021 at 1:49 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Yes, just run recon-all with the -fill option to regenerated the
filled.mgz (it will be the same filled.mgz but it will have a
colortable embedded; it will also create filled.auto.mgz to help
keep track of the edits). The just edit filled.mgz and proceed as
normal. When you edit, make sure you use the right brush value
depending on whether you are editing the left or right subcortical
mass.

On 7/21/2021 1:43 PM, Aaron Tanenbaum wrote:


External Email - Use Caution

Read the release notes.  Can I with the new version run a
recon-all over processed 7.1.1.  I am interested in the ability
to edit filled.mgz and applying this to 7.1.1 recons.

On Mon, Jul 19, 2021 at 5:46 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

We are  please to announce version 7.2. Mostly bug fixes and
behind-the-scenes enhancements. But there are a few new
goodies and one
new "known issue" about defacing. Check out
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes


doug


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Re: [Freesurfer] How to get cortical volume from a particular atlas?

[Douglas N. Greve]

Sorry, we don't support that atlas. Have you tried contacting FSL?

On 9/23/2021 7:08 AM, DRON Noramon wrote:


External Email - Use Caution

Dear Freesurfer Team

I have a very naive question. I am in urgent need to get a cortical 
region volume base on the Harvard-Oxford Cortical Atlas(from FSL). I 
have T1 images in nifti files, brain extracted. How can I get the 
cortical volume using Freesurfer, and regions based on the 
Harvard-Oxford Cortical Atlas? Please, I am very new to Freesurfer and 
in the middle of installing Freesurfer to linux server. Can you tell 
me the steps or a link to your tutorial page? I am trying to find it 
on your wiki page and have trouble navigate around.


Thank you in advance,

Best regards
Noramon
The University of Edinburgh is a charitable body, registered in 
Scotland, with registration number SC005336. Is e buidheann 
carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, 
àireamh clàraidh SC005336.


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[Freesurfer] Customising overlay

[Worker, Amanda]

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Dear FreeSurfer Developers,

I am attempting to create some figures which display regional (Destrieux atlas) 
values which are typically in the range of 0-10. I would like to have an 
inflated brain with those regional values overlaid, for both patients and 
healthy controls. In total there will be four independent figures. The problem 
I am having is that the range of values is different for each overlay e.g. 
overlay 1 regional value range from 0-3, overlay 2 regional values range from 
0-8, which means that the colour scales are on different scales. I would like 
to find a way to manually set the scale to 0-10 for each overlay, regardless of 
the actual values that exist within the overlay file.

I am currently using the below command to load the overlay and then manually 
configuring the colour scale via the custom option, but I cannot add a point 
that is outside the range of values that exist in that overlay. I hope this 
makes sense and I would appreciate any advice you can give on how to achieve 
consistent colour scales for different overlays.

freeview -f 
/software/system/freesurfer/freesurfer-6.0.0/subjects/fsaverage/surf/rh.inflated:overlay=rh_pcnt_neg_control_01.mgz:overlay_method=linearopaque:overlay_threshold=0,5,10

Kind regards,

Amanda
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Re: [Freesurfer] Migrating data from v6 to v7

[Douglas N. Greve]

You don't need the -legacy flag. Just make a copy of your v6 data and 
then run recon-all -all -s subject

It will see and apply your previous edits.


On 9/22/2021 2:14 AM, Amanda Boyes wrote:


External Email - Use Caution

Hi FreeSurfer experts,

Just checking whether anyone has any advice on my query below?

I would greatly appreciate any advice regarding how to incorporate 
masks/pial edited in v6 into the v7 pipeline.


Thanks and best wishes,

Amanda

*From:*Amanda Boyes
*Sent:* Thursday, 16 September 2021 4:37 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Migrating data from v6 to v7

Hi fellow FreeSurfer users,

I am part of a longitudinal project and have a large dataset that has 
been processed in v6.


I have now upgraded to v7 and would like to update my processed data, 
retaining the existing manual masks and pial edits.


I found an old ReconAllChanges page (January 27, 2006, last updated 
2012) referring to this as a “legacy data set” *MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming 
to be* https://freesurfer.net/fswiki/ReconAllChanges 



I have also found a recon-all wiki page (*MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all 
 
last updated 2017) suggesting the use of the following command for 
legacy datasets: recon-all -subject subjectname -all -legacy


Unfortunately, the -legacy flag is not recognised in v7.

I would be grateful for any advice on how to update my existing data 
from v6.0.0 to v7.2.


Thank you in advance,

Amanda

*Amanda Boyes*

/My pronouns are she/her/hers/

PhD Candidate and Research Assistant (Youth Mental Health)
Thompson Institute

USC


Tel: +61 7 5456 3886

_amanda.bo...@usc.edu.au _  | 
usc.edu.au 
__


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Re: [Freesurfer] Confusion about PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.

[Douglas N. Greve]

They are only changed as part of the resampling process (ie, a form of 
interpolation). Volume and surface area are jacobian corrected.


On 9/22/2021 1:24 AM, 周冬跃 wrote:


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Dear FreeSurfer experts:

I use the command recon-all qcache to get file 
sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.


And I am confused that the cortical thickness in this file is measured 
in common space after sub is aligned with the common coordinate system 
or just measured in subject space after changingthe vertex location in 
subject space?


In other words, when a sub is aligned to the common coordinate 
system,the folding patternschanged.But I am not sure if the value of 
cortical thickness measures has been changed during this process?



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Re: [Freesurfer] QDEC command not found

[Douglas N. Greve]

We are no longer supporting qdec

On 9/21/2021 2:15 PM, Fabiola Macruz wrote:


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External Email - Use Caution

Dear freesurfer experts,
I have installed the freesurfer version 7.1.1 in my computer (Mac).
After running the longitudinal pipeline in all the patients, I tried to open qdec for the 
analysis by typing*qdec *and the answer is "command not found".
Could you help me, please?
Many thanks,

*Dra. Fabíola Macruz *
MD from *Faculdade de Ciências Médicas da Santa Casa de São Paulo*
PhD from*Universidade de São Paulo*
Former Research Fellow from***Stanford University*
Former Clinical Innovation Fellow/ Project Leader from***Mass General 
Brigham*

Phone: + 1(650)686-0668 / + 55(11)99571-5906


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Re: [Freesurfer] Freesurfer version confusion

[Douglas N. Greve]

Did the size of the defect change?

On 9/19/2021 8:36 PM, Paul, Rahul wrote:

Hi freesurfer experts,
I was using FreeSurfer v6 for my research. Recently, I started move to 
FreeSurfer v7.2.


I encountered the following issue:

Some patients, that had extra large error (xL error), were running 
fine (recon-all) in freesurfer 6 (it took time, but the process 
finished, and the segmentation was fine too) but in freesurfer 7, same 
patient recon-all encountered the extra large error (e.g., CORRECTING 
DEFECT 35 (vertices=9718, convex hull=1801, v0=40087 Command 
terminated by signal 11) and after couple of hours recon-all exited 
(recon-all -s 8375 exited with ERRORS ). I am not sure why recon-all 
is existing for freesurfer 7.2 and how can I stop that.



Thank you

Rahul

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Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR

[Douglas N. Greve]

Do you see the note: "make sure at least one voxel has a non-zero value 
for each input"? To do this, you can try loading the input into 
freeview, eg,


tksurferfv fsaverage lh inflated -ov h.N0s2_e4pos.10.mgh -fminmax .0001 1
It will come up with a map of the first subject. Scroll through the 
subjects using the "frame" button. Look for one or more subjects where 
the values are 0 across the surface



On 9/15/2021 4:50 PM, Tsiknia, Amaryllis wrote:


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Sorry about that! Here's the full terminal output:

cwd /space/syn01/1/data/MMILDB/MCE_RBS/fsurf

cmdline mri_glmfit.bin --y lh.N0s2_e4pos.10.mgh --fsgd 
./fsgd_omega/e4_positive.fsgd dods --C ./mtx_omega/e4_positive.mtx 
--surf fsaverage lh --cortex --glmdir lh.N0s2_e4pos.glmdir


sysnameLinux

hostname ip27.ucsd.edu

machinex86_64

user mmilrec5

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/space/syn01/1/data/MMILDB/MCE_RBS/fsurf/lh.N0s2_e4pos.10.mgh

logyflag 0

usedti0

FSGD ./fsgd_omega/e4_positive.fsgd

labelmask/usr/pubsw/packages/freesurfer/RH4-x86_64-R600/subjects/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.N0s2_e4pos.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.N0s2_e4pos.glmdir

Loading y from 
/space/syn01/1/data/MMILDB/MCE_RBS/fsurf/lh.N0s2_e4pos.10.mgh


... done reading.

INFO: gd2mtx_method is dods

Saving design matrix to lh.N0s2_e4pos.glmdir/Xg.dat

Computing normalized matrix

Normalized matrix condition is 13.691

Matrix condition is 98.2187

Found 149955 points in label.

Pruning voxels by thr: 1.175494e-38

Found 0 voxels in mask

ERROR: no voxels found in the mask

make sure at least one voxel has a non-zero value for each input



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Wednesday, September 15, 2021 1:19 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR
Can't see the image. Can you just cut-and-paste the full terminal 
output into the email?


On 9/15/2021 3:02 PM, Tsiknia, Amaryllis wrote:


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Dear Freesurfer Team,

I have been struggling with an error using the mri_gmfit command. I 
have been trying to run a simple surface-based group analysis on 28 
subjects testing whether a continuous variable "OMEGA3_457" relates 
to various RSI measures while adjusting for the effects of gender.


This is the error I am getting:

Image preview

and attached is my .fsgd file. The matrix file I am using is testing 
for the following contrast: 0 0 0.5 0.5.


I produced the lh.N0s2_e4pos.10.mgh file using the mri_surf2surf 
command after using mri_concat to concatenate the RSI data for all 28 
of our subjects into a single lh.N0s2_e4pos.00.mgh file. I have also 
attached thetext file (containing all the paths to the subject data) 
that was fed into the mri_concat command.


Any help would be immensely appreciated.

Thank you,

Amaryllis A. Tsiknia
/Imaging Researcher/
Department of Neurosciences
University of California, San Diego
atsik...@health.ucsd.edu 


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Re: [Freesurfer] Customising overlay

[Wang, Ruopeng]

What version of freesurfer are you using? I tried the latest freeview build and 
had no problem inserting colors at arbitrary value for customized color option.

Best,
Ruopeng


On Sep 23, 2021, at 9:00 AM, Worker, Amanda 
mailto:amanda.wor...@kcl.ac.uk>> wrote:

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Dear FreeSurfer Developers,

I am attempting to create some figures which display regional (Destrieux atlas) 
values which are typically in the range of 0-10. I would like to have an 
inflated brain with those regional values overlaid, for both patients and 
healthy controls. In total there will be four independent figures. The problem 
I am having is that the range of values is different for each overlay e.g. 
overlay 1 regional value range from 0-3, overlay 2 regional values range from 
0-8, which means that the colour scales are on different scales. I would like 
to find a way to manually set the scale to 0-10 for each overlay, regardless of 
the actual values that exist within the overlay file.

I am currently using the below command to load the overlay and then manually 
configuring the colour scale via the custom option, but I cannot add a point 
that is outside the range of values that exist in that overlay. I hope this 
makes sense and I would appreciate any advice you can give on how to achieve 
consistent colour scales for different overlays.

freeview -f 
/software/system/freesurfer/freesurfer-6.0.0/subjects/fsaverage/surf/rh.inflated:overlay=rh_pcnt_neg_control_01.mgz:overlay_method=linearopaque:overlay_threshold=0,5,10

Kind regards,

Amanda
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Re: [Freesurfer] Best graphics card for freesurfer?

[Fischl, Bruce]

It is quite likely that in the next year or two we will be releasing versions 
that have GPU support, so getting a card with a reasonable amount of RAM would 
be a good idea

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Tim Schäfer
Sent: Thursday, September 23, 2021 2:45 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Best graphics card for freesurfer?

External Email - Use Caution

FreeSurfer does not require any special graphics card, you can chose whatever 
card you like (as long as it works under Linux, but I haven't come across one 
that did not in the last 10 years or so).

*If* you want to run stuff on the GPU (the current FreeSurfer version does not 
support it afaik, but maybe you have other use cases), an Nvidia card may be 
better because from what I am seeing, CUDA seems to be more widely used than 
OpenCL. If you do not care about CUDA or have never used it, chances are high 
you can completely ignore this.

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy 
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

> On 09/23/2021 8:24 AM Falko Mecklenbrauck  wrote:
> 
>  
> External Email - Use Caution
> 
> Hello Freesurfer Developers,
> 
> the old Linux-Computer Freesurfer was running on broke down and now we 
> need to buy a new one.
> The recommondations in the systems requirements were very helpful, but 
> they seem a bit outdated.
> For Graphics Card it says:
> 
>   * /ATI (AMD) vs nVidia: We still spec nVidia because we don't have
> problems with its OpenGL-X driver under linux. Perhaps ATI has
> finally supplied one that works, but this hasn't been attempted in a
> couple years. ATI cards on the Mac work fine with freesurfer though. ///
>   * /GPU: We no longer support [further] CUDA or GPU development because
> of lack of resources and difficulty, in preference to using OpenMP,
> which uses CPU cores. We will continue to support the existing GPU
> CUDA code that runs on recon-all with the -use-gpu switch. By
> support, keeping it running with each new nvidia cuda driver release
> as best as we can./
> 
> Is this still accurate? The Tech support at my university would order 
> an AMD graphics card, since the issue with the drivers for Linux seems 
> to be fixed. Does anyone has any current experiences with AMD vs. 
> nVidia graphics cards?
> 
> Thanks in advance and best wishes,
> Falko
> 
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[Freesurfer] Confusion about PATH/sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.

[周冬跃]

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Dear FreeSurfer experts: I use the command recon-all qcache to get file 
sub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file. And I am confused that the 
cortical thickness in this file is measured in common space after sub is 
aligned with the common coordinate system or just measured in subject space 
after changing the vertex location in subject space? In other words, when a sub 
is aligned to the common coordinate system,the folding patterns changed.But I 
am not sure if the value of cortical thickness measures has been changed during 
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[Freesurfer] How to get cortical volume from a particular atlas?

[DRON Noramon]

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Dear Freesurfer Team

I have a very naive question. I am in urgent need to get a cortical region 
volume base on the Harvard-Oxford Cortical Atlas(from FSL). I have T1 images in 
nifti files, brain extracted. How can I get the cortical volume using 
Freesurfer, and regions based on the Harvard-Oxford Cortical Atlas? Please, I 
am very new to Freesurfer and in the middle of installing Freesurfer to linux 
server. Can you tell me the steps or a link to your tutorial page? I am trying 
to find it on your wiki page and have trouble navigate around.

Thank you in advance,

Best regards
Noramon
The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh 
Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.
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Re: [Freesurfer] thesegment_T1.sh error

[Iglesias Gonzalez, Juan E.]

Glad to hear!

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Sep 22, 2021, at 16:37, Szulia Agata 
mailto:agata.szu...@stud.umed.lodz.pl>> wrote:


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Dear E,

thank you for the reply. My machine has 8 GB of RAM. It might be that it ran 
out of RAM, I’ve switched to a laptop with only fs installed on it and now it 
works like a charm. Thank you a lot!

Kind regards,
Agata

On 20 Sep 2021, at 13:10, Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>> 
wrote:

Dear Agata,
Is it possible that you may have run out of RAM? How much RAM does your machine 
have?
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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On Sep 17, 2021, at 01:45, Szulia Agata 
mailto:agata.szu...@stud.umed.lodz.pl>> wrote:


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Hi,

I’m trying to run thesegment_T1.sh command on centos 7 in docker (fs 7.2.0). I 
have matlab v2014b installed in fs there. The subjects were successfully put 
through recon-all on mac Big Sur (also fs 7.2.0 but matlab does not want to 
work with Big Sur). I don’t know what to do with the error I get with every 
recon-all’d subject:

Smoothing mesh collection with kernel size 0.75 ...Smoothing class: 0
/usr/local/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
40:   797 Killed  
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML bmat1 
/usr/local/freesurfer/subjects 0. 
/usr/local/freesurfer/average/HippoSF/atlas/AtlasMesh.gz 
/usr/local/freesurfer/average/HippoSF/atlas/AtlasDump.mgz 
/usr/local/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 
left L-BFGS v21 '/usr/local/freesurfer/bin/fs_run_from_mcr 
/usr/local/freesurfer/bin/' 0
Linux 3520b46e7a14 5.10.47-linuxkit #1 SMP Sat Jul 3 21:51:47 UTC 2021 x86_64 
x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Thu Sep 16 23:20:28 UTC 2021

For more details, see the log file 
/usr/local/freesurfer/subjects/bmat1/scripts/hippocampal-subfields-T1.log

If any one of you has run into this kind of problem or know how to solve it, 
I’d be happy to hear your thoughts.

Kind regards,
Agata



Klauzula poufności. Ta wiadomość pocztowa i wszelkie załączone do niej pliki są 
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Re: [Freesurfer] Brainstem segmentation

[Erik O'Hanlon]

External Email - Use Caution

Dear Eugenio,

Thanks so much for your reply. I will certainly follow your instructions on 
"small volume" registration. That will certainly allow us to benefit from the 
more specialized volume showing neuromelanin within the LC area in conjunction 
with the whole brain T1 and brainstem component.

Very much appreciated

Best regards

Erik






From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: Thursday 23 September 2021 03:27
To: Freesurfer support list 
Subject: Re: [Freesurfer] Brainstem segmentation

Dear Erik,

I never put together a multi-spectral version of the brainstem segmentation 
because, given the coarse structures that we segment (midbrain, pons, medulla, 
scp), there’s pretty much nothing to be gained from additional contrasts.

In terms of registration: if your “small volume” is acquired during the same 
session as the 1mm T1 you’ve processed with FreeSurfer, they should be almost 
overlapping in RAS coordinates. You can then use mri_robust_register with the 
—noinit flag to register the volumes. I would strongly encourage you to use the 
small volume as target of the registration and the 1mm T1 as source; you can 
always invert the resulting rigid transform matrix to go in the other direction.

Cheers,

/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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On Sep 20, 2021, at 18:43, Erik O'Hanlon 
mailto:ohanl...@tcd.ie>> wrote:

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Dear Experts,

We hope to acquire some multishell dwi and structural data to investigate 
tracts passing through the Locus Coeruleus (LC) and we want to apply the 
brainstem segmentation to our structural data to obtain subject specific LC 
masks.
Is it possible to feed multispectral data into the brainstem segmentation ?
Is it possible to acquire a high res volume capturing the LC in greater detail 
and co-register that to the whole brain T1 (T2 or FLAIR ) to further assist in 
the delineation of the LC roi and quantification of the LC volume?
If it's possible to use an additional small volume like this, do I need to 
pre-process it using recon-all and what is the optimal way to co-register the 
small volume to the whole brain T1 to assist in the mask generation?

Any guidance is very much appreciated.

Best regards and thanks,

Erik




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Re: [Freesurfer] Best graphics card for freesurfer?

[fsbuild]

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Freesurfer dropped support for CUDA builds because it’s too much work to keep 
up with the compatible combinations of machines, graphics hardware and 
supported CUDA drivers.
Freeview depends upon graphics packages such as Qt and VTK.  My 
understanding is those packages can make use of OpenGL if the version is recent 
enough.   That being said, I thought I read VTK may drop OpenGL in version 
8 or future versions (freeview currently uses vtk version 7).  Looks like 
it is worthwhile to use a graphics card that supports OpenGl version 3 or 
higher (maybe the newest version is up to 4.X ?).  The version numbers for 
OpenCL may be different and I don’t recall what those are up to now.  But 
supporting the newer version of those should be preferable on linux machines.
For MacOS, graphics cards need to support Apple's Metal Framework (since 
Mojave, 10.14.X) and OpenGL has been deprecated.   Apple stopped providing 
Nvidia with the information needed to create Mac graphics drivers and currently 
uses AMD cards.  Consequently only older/used Nvidia cards work with MacOS 
which I suspect support only old versions of OpenGL.  So if you have a Mac 
that allows you to install a graphics card (or you build a Hackintosh), then 
Nvidia cards are not the most up to date choice and you could be better off 
with AMD hardware.
- R.
On Sep 23, 2021, at 02:45, Tim Schäfer  
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   FreeSurfer does not require any 
special graphics card, you can chose whatever card you like (as long as it 
works under Linux, but I haven't come across one that did not in the last 10 
years or so).*If* you want to run stuff on the GPU (the current FreeSurfer 
version does not support it afaik, but maybe you have other use cases), an 
Nvidia card may be better because from what I am seeing, CUDA seems to be more 
widely used than OpenCL.. If you do not care about CUDA or have never used it, 
chances are high you can completely ignore this.Tim--Dr. Tim SchäferPostdoc 
Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, 
Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe 
University Frankfurt am Main, GermanyOn 09/23/2021 8:24 AM Falko Mecklenbrauck 
 wrote:External Email - Use Caution 
   Hello Freesurfer Developers,the old 
Linux-Computer Freesurfer was running on broke down and now we need to buy 
a new one.The recommondations in the systems requirements were very helpful, 
but they seem a bit outdated.For Graphics Card it says: * /ATI (AMD) 
vs nVidia: We still spec nVidia because we don't have   problems 
with its OpenGL-X driver under linux. Perhaps ATI has   finally 
supplied one that works, but this hasn't been attempted in 
a   couple years. ATI cards on the Mac work fine with freesurfer 
though. /// * /GPU: We no longer support [further] CUDA or GPU development 
because   of lack of resources and difficulty, in preference to 
using OpenMP,   which uses CPU cores. We will continue to 
support the existing GPU   CUDA code that runs on recon-all with 
the -use-gpu switch.. By   support, keeping it running with each 
new nvidia cuda driver release   as best as we can./Is this 
still accurate? The Tech support at my university would order an AMD 
graphics card, since the issue with the drivers for Linux seems to be 
fixed. Does anyone has any current experiences with AMD vs. 
nVidia graphics cards?Thanks in advance and best 
wishes,Falko___Freesurfer mailing 
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