Re: [Freesurfer] [EXTERNAL] Re: recon-all hard error: mris_calc could not establish read access to rh.area

[Ariko, Taylor]

External Email - Use Caution

Hello Yujing,


Thank you for your quick response!


When I run:

mris_calc -o rh.area.mid /path/to/subject/surf/rh.area add 
/path/to/subject/surf/rh.area.pial

I get the following error:

error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 
'/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/rh.area'.


But when I run:

mri_info rh.area

I get the following output:

Volume information for rh.area
  type: unknown
dimensions: 831 x 10015 x 25953
   voxel sizes: -0.00, -0.00,nan
  type: SHORT (4)
   fov: 1016.473
   dof: 1
xstart: 0.0, xend: 990983162970892849632569550308376576.0
ystart: -0.0, yend: 3079152361728581627851833344.0
zstart: -0.0, zend: -3815443229699337177012458129513775104.0
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 = 
-18770011487391973376.
  : x_a =   0., y_a =   0., z_a =   1., c_a =nan
  : x_s =   0., y_s =  -1., z_s =   0., c_s =-0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
0.  -0.  nannan
   -0.  -0.  nannan
   -0.   0.  nannan
0.   0.   0. 1.

voxel-to-ras determinant nan

ras to voxel transform:
error: mat = NULL!


It appears that this is where the issue is coming from. Any ideas on why this 
is occurring? The brain is normal and has good rh.white and rh.pial surfaces.


Many thanks,
Taylor


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Date: Tuesday, March 5, 2024 at 4:25 PM
To: Freesurfer support list 
Subject: [EXTERNAL] Re: [Freesurfer] recon-all hard error: mris_calc could not 
establish read access to rh.area
CAUTION: This email originated from outside the organization. DO NOT CLICK ON 
LINKS or OPEN ATTACHMENTS unless you know and trust the sender.
Hi Taylor,

I don’t understand how you could get that error.  It seems to me that 
read_signa() is for reading .signa files.

Can you try ‘mris_calc -o rh.area.mid rh.area add rh.area.pial’ directly? Pass 
full path to your rh.area and rh.area.pial.

What does ‘mri_info rh.area’ report?

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read 
access to rh.area


External Email - Use Caution
Hello FreeSurfer Developers,


I am attempting to run the recon-all pipeline on one subject using the 
following code:

recon-all -all -i t1.nii -s p03_1

Although, I get the following error in the command line:

mris_calc -o rh.area.mid rh.area add rh.area.pial
error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 'rh.area'.

Tue Aug  1 15:58:13 EDT 2023
ERROR: vertexvol
mris_calc -o rh.area.mid rh.area add rh.area.pial
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul  5 
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64

recon-all -s p03_8 exited with ERRORS at Tue Aug  1 15:58:13 EDT 2023

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Re: [Freesurfer] aparc & wm underestimation

[Stanica, Maria]

External Email - Use Caution

Yes, the problem is that the white surface on the left side of the image is 
extending too far into subcortical gray matter. We did delete the control 
points and ran some white matter edits, but the image I sent you is after we 
applied those edits (it was even worse before). I don’t see any other wm edits 
we can make to the image. It didn’t resolve our issue enough to make the image 
usable for our analyses, so I wanted to see if there was anything else we could 
do to resolve the problem.

Thank you!


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

Date: Tuesday, March 5, 2024 at 9:11 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] aparc & wm underestimation
Just to make sure I understand, the problem is that the white surface on the 
left side of the image is extending too far into subcortical gray matter, 
right? This can be difficult to fix, but the right fix is to edit the wm.mgz. 
Make sure to delete your control points as that is not the right fix. Also, 
remember that the surfaces in this area may always be inaccurate if you can see 
where the boundary is.
On 3/3/2024 6:09 PM, Stanica, Maria wrote:

External Email - Use Caution
This is after the most recent round of edits for one of the subjects.

Maria Stǎnicǎ, B.A. | Graduate Student
Medical/Clinical Psychology Doctoral Program
UAB |The University of Alabama at Birmingham
mstan...@uab.edu
Pronouns: she/her/hers
[Image]



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Date: Sunday, March 3, 2024 at 3:38 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] aparc & wm underestimation
Can you send pictures of the slices showing the problem?
On 3/3/2024 3:18 PM, Stanica, Maria wrote:

External Email - Use Caution
Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything processed 
correctly (and exited without errors), except 4 images which have an 
underestimation in coronal subcortical region. The underestimation is 
significant and goes on for about 10-12 slices (for one image it was 153-162, 
for another it was 150-164).

After searching the list, we attempted control points, which ended up not 
working (I don’t believe this was the right method to correct the error). Then 
we tried white matter edits, and one of the images was resolved, but the other 
3 did not get better. Is there anything else we could do to try to resolve the 
issue? I can provide any other information needed. Any help would be 
appreciated!


  1.  Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
  2.  Operating System: Red Hat Enterprise Linux 7
  3.  OS Version: 7.9 (Maipo)

Best,
Maria

Maria Stǎnicǎ, B.A. | Graduate Student
Medical/Clinical Psychology Doctoral Program
UAB |The University of Alabama at Birmingham
mstan...@uab.edu
Pronouns: she/her/hers
[Image]




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Re: [Freesurfer] recon-all hard error: mris_calc could not establish read access to rh.area

[Huang, Yujing]

Hi Taylor,

I don't understand how you could get that error.  It seems to me that 
read_signa() is for reading .signa files.

Can you try 'mris_calc -o rh.area.mid rh.area add rh.area.pial' directly? Pass 
full path to your rh.area and rh.area.pial.

What does 'mri_info rh.area' report?

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ariko, Taylor
Sent: Tuesday, March 5, 2024 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all hard error: mris_calc could not establish read 
access to rh.area


External Email - Use Caution
Hello FreeSurfer Developers,


I am attempting to run the recon-all pipeline on one subject using the 
following code:

recon-all -all -i t1.nii -s p03_1

Although, I get the following error in the command line:

mris_calc -o rh.area.mid rh.area add rh.area.pial
error: No such file or directory
error: read_signa(/Volumes/Beta/Carmen/t1/p03_8/p03_8/surf/I.001): could not 
open file
error: No such file or directory
error:
mris_calc: could not establish read access to 'rh.area'.

Tue Aug  1 15:58:13 EDT 2023
ERROR: vertexvol
mris_calc -o rh.area.mid rh.area add rh.area.pial
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul  5 
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64

recon-all -s p03_8 exited with ERRORS at Tue Aug  1 15:58:13 EDT 2023

To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

The recon-all.error file contains:

--
SUBJECT p03_8
DATE Tue Aug  1 15:58:13 EDT 2023
USER taylorariko
HOST C02F10PVPN5W.local
PROCESSOR x86_64
OS Darwin
Darwin C02F10PVPN5W.local 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul  5 
22:21:56 PDT 2023; root:xnu-8796.141.3~6/RELEASE_X86_64 x86_64
7.2.0 (freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b)
/Applications/freesurfer/7.2.0/bin/recon-all
PWD /Volumes/Beta/Carmen/t1/p03_8/p03_8/mri
CMD vertexvol --s p03_8 --rh --th3

I have made sure that I have read, write, and execute access to the folder 
/path/to/subject/surf and the file rh.area. I can successfully run the command 
to make rh.area (mris_place_surface --area-map ../surf/rh.white 
../surf/rh.area), but the error persists in using rh.area. I have disk space 
and can run other commands such as this fake one (mris_calc -o rh.area.Test 
rh.area.pial add rh.area.pial), but not if it contains rh.area. I have tried to 
rerun the command from root and get the same error message.

I found 2 similar threads of the mail-archive, though I didn't find any 
remedies:

  1.  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44230.html
  2.  MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51444.html

Does anyone have any thoughts on how to trouble-shoot this? I have included my 
recon-all.log in the case it is of any use.


  1.  Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
  2.  Platform: macOS Sonoma 14.3.1
  3.  uname -a: Darwin C02F10PVPN5W.local 23.3.0 Darwin Kernel Version 23.3.0: 
Wed Dec 20 21:28:58 PST 2023; root:xnu-10002.81.5~7/RELEASE_X86_64 x86_64
  4.  recon-all.log: see attached


Thanks in advance!

Taylor Ariko

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The 

Re: [Freesurfer] TRACULA GLM output question

[Douglas N. Greve]

The easiest thing is to set up contrasts to pull out the parameters you 
want. The next easiest (or maybe the easiest) is to look in the beta 
file. It will have a frame for each column in the design matrix. The 
value is the regression coefficient.


On 3/5/2024 11:33 AM, Hoskinson, Kristen wrote:


External Email - Use Caution

We’re working on a project where we ran 3 groups, 1 covariate, and ran 
a glm looking at white matter at cross-sections from TRACULA output, 
covarying for functional activation. We’re now wanting to plot out the 
interaction/slopes per group, but are having trouble locating the data 
that would allow that step.  Could anyone direct us?


Thank you!

--

*Kristen R. Hoskinson, Ph.D. *(she/her)

Associate Professor of Pediatrics

The Ohio State University College of Medicine

Principal Investigator, /Social Cognition, Adjustment, and 
Neurodevelopment (SCAN) Lab/


Center for Biobehavioral Health

The Abigail Wexner Research Institute at Nationwide Children's Hospital

700 Children's Drive
Columbus, Ohio  43205

(614) 722-3021

kristen.hoskin...@nationwidechildrens.org 




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[Freesurfer] TRACULA GLM output question

[Hoskinson, Kristen]

External Email - Use Caution

We’re working on a project where we ran 3 groups, 1 covariate, and ran a glm 
looking at white matter at cross-sections from TRACULA output, covarying for 
functional activation. We’re now wanting to plot out the interaction/slopes per 
group, but are having trouble locating the data that would allow that step.  
Could anyone direct us?

Thank you!

--
Kristen R. Hoskinson, Ph.D. (she/her)
Associate Professor of Pediatrics
The Ohio State University College of Medicine
Principal Investigator, Social Cognition, Adjustment, and Neurodevelopment 
(SCAN) Lab
Center for Biobehavioral Health
The Abigail Wexner Research Institute at Nationwide Children's Hospital
700 Children's Drive
Columbus, Ohio  43205
(614) 722-3021
kristen.hoskin...@nationwidechildrens.org

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Re: [Freesurfer] Citing the bert dataset

[Douglas N. Greve]

Most of the info has been lost for that scan. It was a GE 1.5T scanner; 
subject is a male, approx 37yo


On 3/4/2024 2:49 PM, Shounak Nandi wrote:


External Email - Use Caution

Hi,

I have used the *bert 
*dataset 
in one of the scientific works and was curious how I cite it?


I am eager to know your thoughts.

Thanks,
Shounak Nandi

Radiology Trainee,
Department of Radiology and Radiological Science,
Division of Cancer Imaging Research,
Johns Hopkins School of Medicine,
Baltimore, MD

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Re: [Freesurfer] aparc & wm underestimation

[Douglas N. Greve]

Just to make sure I understand, the problem is that the white surface on 
the left side of the image is extending too far into subcortical gray 
matter, right? This can be difficult to fix, but the right fix is to 
edit the wm.mgz. Make sure to delete your control points as that is not 
the right fix. Also, remember that the surfaces in this area may always 
be inaccurate if you can see where the boundary is.


On 3/3/2024 6:09 PM, Stanica, Maria wrote:


External Email - Use Caution

This is after the most recent round of edits for one of the subjects.

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu 

Pronouns: she/her/hers

Image

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


*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything
processed correctly (and exited without errors), except 4 images
which have an underestimation in coronal subcortical region. The
underestimation is significant and goes on for about 10-12 slices
(for one image it was 153-162, for another it was 150-164).

After searching the list, we attempted control points, which ended
up not working (I don’t believe this was the right method to
correct the error). Then we tried white matter edits, and one of
the images was resolved, but the other 3 did not get better. Is
there anything else we could do to try to resolve the issue? I can
provide any other information needed. Any help would be appreciated!

 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
 2. Operating System: Red Hat Enterprise Linux 7
 3. OS Version: 7.9 (Maipo)

Best,

Maria

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu 

Pronouns: she/her/hers

Image



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[Freesurfer] 2 PhD positions in layer-fMRI of high-level cognition at the Max Planck Institute for Biological Cybernetics in Tübingen , Germany

[Romy Lorenz]

External Email - Use Caution

The newly established Cognitive Neuroscience & Neurotechnology group led by Dr. 
Romy Lorenz is looking for two enthusiastic PhD students (m/f/d) to join our 
growing team at the Max Planck Institute for Biological Cybernetics in 
Tübingen, Germany.

Our lab focuses on advancing our understanding of the frontoparietal brain 
network mechanisms that underpin high-level cognition and adaptive behaviour. 
For this, we pursue an interdisciplinary research programme that allows 
studying this brain system at multiple levels of granularity. Our methodology 
involves subject-specific brain-computer interface technology, fMRI at 3T and 
ultrahigh (i.e., 7T and 9.4T) magnetic field strengths (for resolving cortical 
layers), EEG, non-invasive brain stimulation as well as machine learning. You 
can find out more about our work at:
https://secure-web.cisco.com/1DTFYMuBJpaThDmnsZx8BTzF2AVMPT_WTXTuNSPnfZdIr4LT02Uwr7NiWM-keXllcKTwvWRCbvu-J8hN2Vm2bKKGpIcY2K51wkuyS3hk-IKV_Tz558f5_k7vTrQM_fb2TqZNzOZTlk3jSrVFJ8MgYZoFSfWFOyip0hrqOe1ckcUdZP4xe1ifVWj40R-s9r3ngAEWdq4YXfbHCEzvgfnXEJUetbh8BKXmzeH-j-aDQ7i6aFIAW4k4FBGvCnJ8EEwX4WDRjozyhDYIVlYV7As61X5pvh7J4KAWHV0O_fMZwTxv9x6_5EDUl3zi4MLLBEbBiF1DcU3epMBTcFr9tIhkFeA/https%3A%2F%2Fwww.kyb.tuebingen.mpg.de%2F711763%2Fcognitive-neuroscience-neurotechnology

We are seeking two ambitious PhD students who will work on the exciting field 
of ultrahigh resolution fMRI that allows to investigate the human cortex at the 
scale of layers and columns. 

The ideal candidates should have a master’s degree in cognitive (neuro)science, 
psychology, computer science, biomedical or electrical engineering, physics, or 
related disciplines. A strong background in fMRI data analysis (e.g., FSL, 
Freesurfer, ANTS) and very good programming skills in Bash on Linux, Matlab 
and/or Python are required. Prior experience in MRI data acquisition and 
experience with ultrahigh resolution fMRI (e.g., at 7T) is desirable but not 
necessary. Equally, experience with machine learning-methods, code sharing 
platforms (e.g. GitHub) and high-performance computing clusters are highly 
desirable.

The Max Planck Institute for Biological Cybernetics offers a world-leading 
research environment with access to the latest cutting-edge MRI hardware 
(including a Siemens 9.4T and Prisma 3T for humans as well as a 14.2T small 
animal system) and other excellent research facilities (EEG, eye-tracking, 
fMRI-TMS). The PhD student will receive generous support for professional 
travel and research needs (~2500€/year). Additionally, the student will have 
the opportunity to become part of the Graduate Training Centre of Neuroscience 
that provides training courses, summer schools and conferences to further 
educate doctoral students. Further, the Institute is part of the 
TübingenNeuroCampus (with more than 100 active groups), offering a vibrant 
community of international researchers and enriching environment of 
collaboration.

The position is available from May 2024 on and remains open until filled. The 
salary is paid in accordance with the collective agreement for the public 
sector (65% TVL-E13, amounting to ~2000€ net per month).

For more details about the two advertised PhD positions and how to apply, 
please see: 
https://secure-web.cisco.com/1HBQhEBJ4wZ9IS2zpkXMkuIwzjxkS5db6bDYMd0qWJKNhnqMPJRNqQ_-5UPT6tspJQjjqs42PNHOs9hxq_qoC5AVBJOhE6J7TNC0GRqq96dTIG75XuBmvL_lViOs6zb1DpJpTk0abpceOXgIoRosjBSBDGyaSUDbwxGKPpZaJBZgyG6fxUuQlUdZmcSSyuSXTPE_ucfRdTIk02LP45wmJ3rtoMZOsrlJhtruf5OShc0NXxknbpmoL5Rb7lMcZldF4W2oag5lPN-e6r___q0vH66qTX37RSkL-EJU6_xkd9qLjnYmjZZfBenk5VkYeAqeTuq_RNjJ-PbKhJWEpDGJ5jQ/https%3A%2F%2Fwww.kyb.tuebingen.mpg.de%2F729399%2Fjoin-the-lab

 

Dr. Romy Lorenz


Max Planck Research Group Leader 

Research Group Cognitive Neuroscience & Neurotechnology

Max Planck Institute for Biological Cybernetics

Tübingen, Germany

romy.lor...@tuebingen.mpg.de

http://secure-web.cisco.com/1-aUWpt7JdIbcqswpTsDWYsyChmNmUZeOBqxYreWQN848TotOom1FPfUZwyy6Rp2pc5T7a84j3jY9xUhJMRjLTC_D_WySXcoBdFYaG-hTzPEwXR4VW9TgNrNVhyBcpNnRZ69mU4wRRJ6iApywf3WOG8V9rOMlt7R1L8AnI2FLZfuDomFIUvNEbyNl2QgQ1u9ztjkyq76S6POaRcrV7cWzlfnZqovZ0IEJDiwu7pRkdbT2AcW4xWF9XFGY3Rq2XbZm2WjDeoeWkCTTEHgIz7VsJXwPnSR1LswFxGrEF46Ytp78WnsGnP_RvfNUljkjciwXV54QE_nZoFCbTFBquI67xw/http%3A%2F%2Fwww.kyb.tuebingen.mpg.de%2F711763%2Fcognitive-neuroscience-neurotechnology

 

 

 

 

 

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Re: [Freesurfer] Assistance Request: Issue with Merging .mgh Files in Ubuntu18

[Rosie]

External Email - Use Caution

Hi Yujing, 
Thank you so much for your help. It works well!
Cheers,
Rosie




At 2024-03-01 21:39:02, "Huang, Yujing"  wrote:

Hi Rosie,

 

Are you trying to combine all volume files (.nii.gz) into one single volume by 
stacking all frames? Maybe you should use Freesurfer mri_concat instead of 
mrcalc?

 

Here are the help pages for mri_concat and mri_vol2surf:

 

https://secure-web.cisco.com/1tLcusmOJJpls_HMuxOKJJmKCYKR_Ppkbo1C4mLApp-4lMHJJZZmI5AxGitZB_66ceS4m-V2l061ljcKGhq9CDUUYwYv-a3-02omLvfID7wnNVDTR6tE0T-bByxfKTxx30WZjrfEe_pdotF4yJhzco8WClGA4jHwBnP2e14rAs4SMWyX_A4lSuDrlTwYRKKSPFHc-SeFfrATCZ8wvGS002wN3wtfO1ZRKcNpvJGOigMWut_k2lhBA0mZhpJr6AIJsuy_qdipPmBj-eKpnUYTkmwfNg1SUygQINgtq2S8tWGubL00W-kqDVc6jkQ58g1PeWYdHMZlksAA_TuQMpiKIuQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_concat

https://secure-web.cisco.com/1dNBwTwslJ7ddeVw34J9pR8X5ecwtAz43umMNRC7GAnKcRahGL-UVWskpllrdKewG4AYAFvAXIgfwU1T7aO_LHzGgcFpSTMlEc8Ckg6yRdzcRyevZpOylpL9Y__-Svc9B8e8t-rZ6GBjL3mDaLA2311F46wwzrSHN_1uHxm3bRXf4s-rxoqVtdsu4z_j-aX3xV8HLbKmreqbFXig5GNwjPPPaoX3GSjKORDETG3Cxag_TaPe3CAdtakPR2SzPwFu75MNgyagNPyIiXWfjO93Jc4PPOCtNujAN6kagk8EONvyGeG_pW5UgdWGfUDMqODDX-0iKRIJccme5pIpaEjhjuQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_vol2surf

 

 

Best,

 

Yujing

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rosie
Sent: Thursday, February 29, 2024 10:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Assistance Request: Issue with Merging .mgh Files in 
Ubuntu18

 

External Email - Use Caution

Dear Support Team,

 

I'm reaching out for assistance with merging two .mgh files.

 

As I try to generate a surface mapping for all subjects, I merged all volume 
files (.nii.gz) by mrcalc. So I get a volume file whose voxel value represents 
the number of valid subjects. And then I convert it to .mgh using mri_vol2surf. 
But the value of each voxel seems to be thrown out. Because I found the max 
value of .mgh is not the same as .nii file.

 

I guess I should merge files of all subject in mgh format to maintain the 
number of valid subjects, but it seems to be a volume encoded surface file 
format. So I don't know how to merge them.

 

I'm working on Ubuntu18. 

 

I would be very grateful for your assistance. 

 

Best,

Rosie

 

 

 

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