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Dear list,
I have some points of interest (volume coordinates, e.g. '5.9, -27.7, 49.7') in
MNI152 space. I would like to transform them to fsaverage space.
How should I do that?
I noticed that FreeSurfer comes with the file
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Dear FreeSurfer experts,
I have a raw nifti file created from a stack of DICOM scanner images, let's say
it has dimension (162, 172, 188) along the 3 axes. I have also pre-processed
this subject in FreeSurfer and have the resulting volume files
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What are $label and $input set to?
> On January 2, 2019 at 9:13 PM Tamara Sussman wrote:
>
>
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>
> Hello Freesurfer Experts!
>
> Thank you in advance for considering this question.
>
> I did a
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One last thing I forgot: you could maybe check whether you can get access to
some super computer. Maybe some university you know has one and you can request
access (maybe even for free).
It's nice to have your own server, but access to a 2nd system
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I would not recommend to buy a notebook to run FreeSurfer. If you want to run
many subjects, it takes a lot of time (between 10 and 20 h per subject and
processor roughly), so you want many cores and also roughly 2GB of RAM per
subject that you are
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Dear Bruce,
thanks for the answer, makes sense. I just wanted to ask: does any FreeSurfer
tool solve the same problem? Because if so, I guess it would make sense if my
code used the same algorithm.
Tim
> On December 20, 2018 at 5:54 PM Bruce
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Please see this recent email from the list archives, I think it is what you are
looking for:
Tim
>
>
> Hello Joseph,
>
> Try this link for the 3rd party libs (to use with the cmake build)
>
>
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Dear FreeSurfer experts,
given a voxel in the cortex of the fsaverage subject, I would like to find the
vertex on the surface that corresponds to the voxel (e.g., if volume data would
be projected to the surface).
I found the documentation at
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K and H are the Gaussian Curvature and the Mean Curvature. Both can be computed
based on the 2 principal curvatures k1 and k2 of a surface.
K and H are not identical to the folding index, though they are related to it
via k1 and k2. k1 and k2 are
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Unless I'm mistaken, the runtime on the FTP should be identical to the one
distributed by Mathworks? Maybe someone who knows can comment on this, but you
could try this link:
https://www.mathworks.com/products/compiler/matlab-runtime.html
Just
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Dear FreeSurfer experts,
I'm parsing data from FreeSurfer stats files, e.g.,
/stats/lh.aparc.stats and aseg.stats.
My question: when parsing measure lines, which combination of fields are
guaranteed to uniquely identify a measure? Here are two
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Without the full command line and error message it is hard to tell, but this
may be an issue with the System Integrity Protection of Mac OS. Try turning it
off and see whether that helps.
Tim
> On December 13, 2018 at 10:05 AM Jaime Gomez wrote:
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We had the same problem. This is related to a "security" feature Apple
introduced some years ago, called "System Integrity Protection".
Turn it off and you will be fine. Basically follow these instructions from
Apple:
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Just to be sure, could you also post the output of the following command:
who am i; ls -ld /usr/local/freesurfer/subjects/groupstudy/
I suspect that you do not have write access to /usr/local/. Unless you are
running FreeSurfer as root (which you
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That looks fine. You are logged in and you changed the directory. Just put the
file now:
put
(In general the command depends on your FTP client, but a 'put' command should
be available in every FTP client I guess.)
A general note: you may be
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Sounds like you do not have the tcsh shell installed on your system. There is
no need to change your default shell from bash to tcsh, but you need tcsh
installed for FreeSurfer to work.
Have your system admin install it. Since Mint is Debian-based,
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Dear FreeSurfer experts,
we would like to use the 'Segmentation of hippocampal subfields and nuclei of
the amygdala' feature [1] that is available in the development version of
FreeSurfer.
However, we already pre-processed all subjects from the
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Dear Mahshid,
could you provide some more details on what exactly is not working? E.g., Did
the installation complete without errors? What command are you typing, what
result do you expect and what is the actual result / error message?
> On
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As you said, you can load FreeSurfer data (both the surface files and volume
data) with the respective nibabel functions, i.e., read_geometry and
read_morph_data. The ?h.pial and ?h.white files are surface meshes, so
read_geometry would apply.
I'm
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Thanks for your time and the clarification.
Tim
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
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Dear Douglas,
thanks for your answer.
Did you by any chance mean mris_preproc instead of preproc-sess? The latter
seems to have no --meas flag according to the help (and a quick grep through
the script file).
I ended up placing the curv files in
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Nevermind, I found in the source code of recon-all (line 180) that you have to
specify the measure as '-measure area.pial' instead of '-measure area' in this
case.
Sorry for the noise.
Tim
> On October 22, 2018 at 11:23 AM ts...@rcmd.org wrote:
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Dear FreeSurfer experts,
I would like to know how to (re-)generate the files
'lh.area.pial.fsaverage.mgh' and 'rh.area.pial.fsaverage.mgh' for a subject (in
the surf/ dir).
I have tried the following:
1.) ensured that the source files, lh.area.pial
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Could you send the output of the following command, please:
ls -l /fileserver/projects/Nian/New3DEDSR20181006/result/1/expert.opt
Tim
> On October 20, 2018 at 12:22 AM Nian Rui wrote:
>
>
> External Email - Use Caution
>
>
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Dear FreeSurfer experts,
I have created a custom measure on the pial surface of a number of subjects,
and I would like to map the data to the fsaverage subject. (By custom measure I
mean something like 'area' or 'curv', i.e., one scalar value per
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Looks like, it the output of that command is `diffcount 0`.
If you binary-diff them you see some differences near the start, but that's
most likely just header info like creation time or something.
Ok, that answers my question. Thanks for your help!
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Dear FreeSurfer experts,
what is the difference between the following 2 files found in a subject's surf/
directory:
* file #1: lh.area.fsaverage.mgh
* file #2: lh.area.fwhm0.fsaverage.mgh
I see in the logs (/scripts/recon-all.log), that file #2
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I you want to get FreeSurfer 6, just download it from the website:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Maybe keep a copy of the installer around for the next machine you want to
install it on, as the download is quite
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I guess this: https://surfer.nmr.mgh.harvard.edu/fswiki/QATools
But it's outdated, I also gave it a try recently and tried to contact the
author without success. It worked for v5, but is not compatible with v6 output.
(If you search the list
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> On September 20, 2018 at 9:12 PM std...@virgilio.it wrote:
>
>
> External Email - Use Caution
>
> I'm using last version dev with MacOS High Sierra 10.13.6.
>
> I have run, for each subject:
>
> segmentThalamicNuclei.sh
>
I
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Dear Andrade,
I've only had a brief look at some parts of the FreeSurfer source code, but as
I've worked as a software engineer for a while, maybe some more general
comments on your thoughts:
On the idea of translating the source to C++: I highly
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Hi Tom and Zahra,
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> on behalf of Tom Parker
>> I am attempting to download the FsPalm patch
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm)
> On September 7, 2018 at 4:10 PM "Nasiriavanaki,
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Dear FreeSurfer experts,
Which tools would you recommend to compute quality metrics for FreeSurfer 6
output?
I would like to complement visual QC of the FreeSurfer segmentation output for
structural images with automated metrics, e.g., outlier
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