External Email - Use Caution
Hey Sebastien,
I'm not sure how to do this in FreeSurfer (mri_add_xform_to_header might work)
but you can overwrite the header in python using nibable. You'll have to
compute the vox2ras yourself however.
Let's say you have image 1 and image 2 and
Hi Peter,
recon-all produces an estimate of ICV. In aseg.stats there is a line that
looks like:
# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial
Volume, 1696008.240403, mm^3
You can read more about how it is computed at
Hi Mahdi,
I'm afraid I don't know what you mean by "Freeview opens fine but when I load a
column in it just shows a black view." What is a column in this context?
As for registration between PET and MR, have you seen this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
It suggests
External Email - Use Caution
Thanks for this, R!
Monika (cc'd) is running into the same issue, and has followed these steps, and
can now open files from the command line, but not from the GUI.
Any ideas?
-Paul
From:
Hi Raffaele,
There is some info here:
https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide
For more details on compiling FreeSurfer from source, you can refer to this
neurodocker template:
Hi Victor,
If you have the original DICOMs you could try something like pydicom to
overwrite the voxel values. The process would go something like:
1) Convert DICOM to nifti using your favorite tool
2) Deface niftii data using your favorite tool
3) Load the defaced data into python using
Hi Katie,
FreeSurfer operates mostly in "FreeSurfer Space", which is voxel resolution of
1mm^3 and sagittal orientation.
You can compare orig.mgz to the original input to see what the difference
between native space and FreeSurfer Space would be.
eTIV is computed using the transformation
of Wighton, Paul
Sent: 30 June 2022 17:36
To: Freesurfer support list
Subject: Re: [Freesurfer] Problem with sxconcat-sess
Hi Noah,
These dof files were not created by recon-all. I was hoping there would be
other log files in the scripts directory describing the functional analysis.
I have
Hi Rachel,
Are you trying to run tkregister2? Looks like you forgot the t at the start of
the command.
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Rachel Wagner
Sent: Tuesday, June 28, 2022 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu
@nmr.mgh.harvard.edu
on behalf of Wighton, Paul
Sent: 28 June 2022 11:10
To: Freesurfer support list
Subject: Re: [Freesurfer] Problem with sxconcat-sess
Hi Noah,
I'm not super familiar with the functional stream, but it looks like something
has gone wrong during the first-level analysis for some of
Hi Ela,
It looks to me like line 79 of bedpostx_preproc.sh is:
if [ ${gflag} -eq 1 ]; then
Which is consistent with the error:
-eq: unary operator expected
What this error is saying is that the variable `gflag` has not been set, so the
script does not know how to perform the comparison.
Hi Marina,
I believe mris_left_right_register can do this.
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Marina Fern?ndez
Sent: Tuesday, June 7, 2022 4:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] vertex ID in the
Hi Noah,
I'm not super familiar with the functional stream, but it looks like something
has gone wrong during the first-level analysis for some of your subjects.
Can you compare the log files in the ./scripts directory for a subject that has
the dof files vs a subject that doesn't and post any
recon-all
is running fine now.
Thank you!
Joanna
--
Joanna Eckhardt
Neurosciences Graduate Program
University of California, San Diego
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Wighton, Paul
Sent: Thursday, May 5, 2022 1:26 PM
To:
Hi Joanna,
Is it possible you've run out of disk space? What's the output of `df --si`?
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Joanna L Eckhardt
Sent: Friday, May 6, 2022 12:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
urfer-boun...@nmr.mgh.harvard.edu
on behalf of Wighton, Paul
Sent: Friday, May 6, 2022 10:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all Error: "ln: failed to create symbolic link
'lh.white.H': Operation not permitted"
Hi Joanna,
Is it possible you've run out of disk space
There's a small percentage of subjects that need more than the 8Gb of memory
(for mris_fix_topology if my memory is correct).
You could increase the memory allocation for all subjects, or you could run
your entire dataset with 8Gb per subject, then re-run the ones that failed with
increased
Hi Joana,
There are a few things going on here.
First, you should create a subjects directory for FreeSurfer recons and tell
FreeSurfer where it is by setting the SUBJECTS_DIR environment variable. You
should be able to do that with these 2 commands:
```
mkdir -p
I just made a PR to neurodocker to support FreeSufer 7.3.2
https://github.com/ReproNim/neurodocker/pull/469
And used that to build the container `pwighton/freesurfer:7.3.2`. I'm pushing
it to dockerhub now. It should be available in an hour or so. It hasn't been
tested yet, so if folks use
ri, Oct 14, 2022 at 12:54 AM Wighton, Paul
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Padma,
It can't find the file:
/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz
Are you trying to run this on a subject called sub-AD003S1059S61129? If so,
can you try:
mri_compute_vol
Hi Padma,
There is probably a 'cleaner' way to do this, but this should work:
cat aseg.stats |grep -v '#'|sed 's/ \{1,\}/,/g'|sed 's/^,//'|sed 's/,$//' >
aseg.csv
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of priya padma
Sent: Wednesday,
Hi Padma,
You can use the --like flag of mri_convert to convert the output of the skull
stripping back to the dimensions of the original file
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert
e.g
mri_convert --like input-to-skullstrip.mgz output-from-skullstrip.mgz
?
Thank you so much for your time.
Sincerely,
Justina
On Tue, Sep 13, 2022 at 9:05 PM Wighton, Paul
mailto:pwigh...@mgh.harvard.edu>> wrote:
I think we are on the right track, but it looks like there was a space between
FREESURFER_HOME and the equal (=) sign? It also looks like there was no
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Wighton, Paul
Sent: Thursday, September 15, 2022 9:56 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
Hi Justina,
Ok so on your computer, the subjects are located
learning student of
linux system) how I can move these files instead of through my computer
manually? Does the problem lie somewhere else?
Thank you and I appreciate your time and efforts.
Sincerely,
Justina
On Wed, Sep 14, 2022 at 5:07 PM Wighton, Paul
mailto:pwigh...@mgh.harvard.edu>> wrote
for this?
Sincerely,
Justina
On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,
Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?
Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr
R2019b`?
: command not found
The same problem persists yet again :( Does the problem lie somewhere else?
Sincerely,
Justina
On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul
mailto:pwigh...@mgh.harvard.edu>> wrote:
Ah ok, let's try this:
cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFE
Hi Justina,
It looks like the matlab installer is trying to use unzip but it can't find it.
Can you try running:
`sudo apt-get install unzip`
To install unzip then try the matlab installer again?
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf
Hi Rüdiger,
This is really interesting.. I'm able to reproduce this issue in a docker
container. Anyone else who would like to reproduce or look into this issue can
use the following containers
- The container `pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16.04
(glibc v2.23) and
with my follow-up issue, I appreciate it a lot.
Thank you so much.
Sincerely,
Justina
On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,
It looks like the matlab installer is trying to use unzip but it can't find it.
Can you try running:
Thanks R, those are very good points.
-Paul
From: fsbuild
Sent: Tuesday, September 13, 2022 2:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: r.lud...@eni-g.de ; Wighton, Paul
; fsbu...@contbay.com
Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
: command not found
I'm terribly sorry for the inconvenience.
Sincerely,
Justina
On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,
Ok so it looks like the install script is getting further and has extracted the
matlab runtime envir
Hi Panos,
Yes that is correct. Taking a voxel value and multiplying it by the vox2ras
matrix will give you a coordinate in the "patient coordinate system" which is
in mm. RAS denotes that the directions (R)ight, (A)nterior and (S)uperior are
positive.
-Paul
Hi Padma,
It looks like tcsh isn't installed. Can you try installing it by running
```
sudo apt update
sudo apt install tcsh
```
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of priya padma
Sent: Wednesday, October 12, 2022 3:16 AM
To:
Hi Padma,
It can't find the file:
/Applications/freesurfer/7.3.2/subjects/tester/mri/aseg.mgz
Are you trying to run this on a subject called sub-AD003S1059S61129? If so,
can you try:
mri_compute_volume_fractions --o test --regheader sub-AD003S1059S61129
/mri/norm.mgz
-Paul
w does not seem to work at all. (For example, trying to run the command
freeview -v T1.mgz does not produce a freeview to open up on another window.)
Could you help me with this? I'm sorry for the troubles once more.
Sincerely,
Justina
On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul
mailto
for the help!
Sincerely,
Justina
On Fri, Sep 30, 2022 at 4:18 PM Wighton, Paul
mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,
I don't know too much about FreeView, unfortunately. Hopefully others on the
list have some ideas.
Are you trying to run FreeView inside the FreeSurfer v
Hi Leema,
This is a known issue. It has to do with the behaviour of the crypt() function
provided by glibc, which has changed in more recent versions of ubuntu. We
don't have a solution for it at this time, unfortunately.
If you downgrade to ubuntu version 16.04 (glibc v2.23) the license
Hey FreeSurfer aficionados,
Is there a FreeSurfer equivalent to fslsplit? If I have a 4d nifti, is there a
way to split that into a set of 3d niftis from the command line?
Thanks,
-Paul
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
mri_convert can take a frame number. Something like:
mri_convert -nth 0 image.nii frame0.mgz
mri_convert -nth 1 image.nii frame1.mgz
.
.
.
Although that means you have to know how many frames are in the original file
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Wighton
(possibly using HCP/UKbiobank to train my model etc).
A colleague has recommended using datacamp to learn machine learning and coding
in python. I was wondering whether there were any other resources that may be
useful?
Kind regards,
Felicity
On Wed, Dec 7, 2022 at 7:33 AM Wighton, Paul
Hi Rahul,
There is are a lot of resources on the "Teach Youself FreeSurfer" page
https://surfer.nmr.mgh.harvard.edu/fswiki/TeachYourselfFreeSurfer
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Rahul Sharma
Sent: Tuesday, December 6, 2022
Hi Chris,
What version of FreeSurfer are you using? There are some issues with the
license file with really old (<6.0) versions, but the 5.3-HCP version should
work.
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/
-Paul
From:
4175583741%2F>
This article is more geared towards remote debugging, but might give you some
insight, https://www.scm.com/doc/Installation/Remote_GUI.html
- R.
On Mar 16, 2023, at 19:19, Wighton, Paul wrote:
Hi All,
I have a colleague who is trying to use FreeView on Red Hat En
then apply to the overlays.
-Paul
From: Anam Anzak
Sent: Wednesday, March 15, 2023 3:52 AM
To: Wighton, Paul; Freesurfer@nmr.mgh.harvard.edu
Cc: Bernardo Pimentel
Subject: Re: Flipping Thickness Matrices
External Email - Use Caution
Dear Paul
Hi Anam,
Check out mris_left_right_register. It's not super well documented, but it
takes as input the right and left hemispheres, inflated onto a sphere, and
outputs the left hemisphere registered to the right and the right hemisphere
registered to the left, also inflated onto a sphere.
If
Hi Vittal,
I tested your license file and it's fine. Are you sure it's in the right
place? What's the output of `cat /usr/local/freesurfer/license.txt`?
It also looks like QDEC is trying to write to
`/usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh` do you have
permissions to
Hi Juan,
It is possible, but not recommended because differing versions of FreeSurfer
will introduce biases into the analysis.
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Juan Rivas
Sent: Thursday, February 23, 2023 10:00 AM
To:
Hi Bennet,
I've been doing my best to support building FreeSurfer containers via
neurodocker (https://github.com/ReproNim/neurodocker).
This template should give you a good idea of the pre-reqs for a FreeSurfer
container.
Hi Gonzalo,
Download the .tar.gz files for the versions you're interested in and extract to
different directories.
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/
Then to run a particular version, set the environment variable FREESURFER_HOME
to the install directory of version you
External Email - Use Caution
Hi Daniel,
It's been a while since I looked into this, but I think you'll need to use
`lta_convert` to convert your lta to xfm format, then use
`mri_add_xform_to_header` to overwrite the header of your phase map.
You might have to extract the
External Email - Use Caution
Hi Zeyu,
It looks like your files are in 'interfile' format.
If you have access to pmod, you might be able to use that to convert your files
to nifti.
appending that to $LD_LIBRARY_PATH didn’t help. Any other tricks? Thanks so
much!
Regards,
Xiaoxu
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Wighton, Paul
Sent: Thursday, December 7, 2023 10:35 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b
Hi
for LGI, will you please kindly let me know
and I’ll give it a try too? Thank you so much!
Regards,
Xiaoxu
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Wighton, Paul
Sent: Thursday, December 7, 2023 11:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR
Hi Xiaoxu,
This is how I built a FreeSurfer 7.1.1 container with matlabmcr 2014b
(https://github.com/pwighton/fs-docker/blob/master/notes/20201127-fs711-neurodocker-min.md#freesurfer711)
```
neurodocker generate docker \
--base continuumio/miniconda:4.7.12 \
--pkg-manager apt \
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