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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?
>
To answer my own question, this seems to be explained as
from the raw file to the
> > Freesurfer pre-processed version (which is resampled to dimension (256,
> > 256, 256) among other changes)
> > - then get and apply the matrix that leads from the pre-processed subject
> > to fsaverage
> >
> > But where exactl
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I do not have experience with running on Google Cloud, but from what I know,
the common way is to run FreeSurfer in parallel over many subjects instead of
using openmp to speed up the process for a single subject.
So your desktop should run 4 subject
t; space.
>
> If you are indeed looking for a transformation between MNI152 volumetric
> space and fsaverage surface space, you can consider the following:
> https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion
>
> Regards,
> T
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Dear FreeSurfer experts,
I have 2 questions on the talairach.m3z file generated by recon-all.
1) What exactly does it contain? I read its the displacement field for a
non-linear transform from native space to some freesurfer space. But from which
in
External Email - Use Caution
The release notes mention this message:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
under 'Known issues' and recommend you run 'sudo -E fs_update'.
> On February 13, 2019 at 1:45 PM Shachar Gal wrote:
>
>
> External Email - U
External Email - Use Caution
That being said, this did not help in my case. I had to disable System
Integrity Protection.
> On February 13, 2019 at 2:08 PM Tim Schäfer wrote:
>
>
> External Email - Use Caution
>
> The release notes me
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Dear Daniel,
your emails do show up on the list, see
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/maillist.html
Here is your last email, for example:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61484.html
Best,
> O
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Dear list,
I would like to register volume data from several subjects to a common volume,
e.g., the volume of the fsaverage subject.
The volume data contains some marked voxels and is in the same space as the
orig.mgz of the respective subject. I w
confirm that this makes sense, I'd still be grateful. ;)
> On February 22, 2019 at 11:27 AM Tim Schäfer wrote:
>
>
> External Email - Use Caution
>
> Dear list,
>
> I would like to register volume data from several subjects to a common
> volume, e
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Hm, I'm not an expert, but the log says 'XL defect detected...'.
I've seen this error on 2 or 3 subjects I tried to process (out of several
hundreds). Usually it happened only when the source images looked very bad even
by a quick visual inspection
, out of curiosity: it is obvious why one should not use different
Freesurfer versions, but what are the reasons for the reported differences
between architectures/workstations?
[1] https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038234
Tim
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Postdoc
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Dear Chenfei,
To successfully use the 'recon-all -qcache' command you listed, you would need
to have the fsaverage4 subject in your $SUBJECTS_DIR. Did you copy it there
before running the command? You can find it in
$FREESURFER_HOME/subjects/fsaver
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Maybe you already know this, but just in case: mris_compute_lgi is a shell
script, so you can open it in an editor and check what it does.cat
The output of the following command gives a good first impression:
cat `which mris_compute_lgi` | grep -
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You could load the aseg in freeview and navigate to the voxel (you can enter
the CRS at the bottom, no need to scroll there). Then you have its intensity
value, which you can check against FreeSurferColorLUT.txt.
Tim
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> On March 13, 2019 at 9:18 PM Donatienne Van Weehaeghe
> wrote:
> The code I tried to run:
>
> #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg
> /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o
> gtmpvc.output.su
mreuter Exp $
> Linux ian-Sabre-17WV8 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6
> 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
> Thu Mar 28 14:33:45 GMT 2019
> Program nu_correct, built from:
>
>
>
> --
> Ian Hardingham
>
>
> __
Department
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for a model with vertex colors that I exported to PLY and
then loaded into Blender here: https://vimeo.com/325645975
In that video, the color is rather uninteresting (it's the surface area at each
vertex), but you can see that it works.
Best,
Tim
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Dr. Tim Schäfer
Postdoc Com
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Dear list,
I have two questions on mris_curvature command line options:
1) the '-a' option, help text is: '-a : perform iterative averages
of curvature measure before saving':
Afaik, this is a smoothing operation. But what exactly is averaged?
2)
t;
> Hi Tim
>
> 1) this is iterative averaging on the mesh, which approximates Gaussian
> in the limit. So -a 2 means average twice.
>
> 2) -nbs N means N hops on the mesh. 1 would be just nearest neighbor
>
> cheers
> Bruce
>
> On Wed, 3 Apr 2019, Tim Schäf
t; here are the outputs for the directories.
> 1) /home/brain/freesurfer
> 2)-rwxr-xr-x 1 brain brain 20569 Jun 19 2015
> /home/brain/freesurfer/mni/bin/nu_correct
>
> Any idea? I've tried it on several datasets and still the problem, though
> the example data sample-001.nii.
urfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
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Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main,
these measures. But it is not clear to
me whether I could use it for a custom surface as well (and if so, how).
Best,
Tim
[1] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent
r for you and you can grab it from dev
>
> cheers
> Bruce
>
>
> On Tue, 14 May 2019, Tim Schäfer wrote:
>
>External Email - Use Caution
>
> Dear list,
>
> I have created a custom surface at 50% thickness between the white and pial
> for my subject
going on?
>
> Thank you very much.
> Best,
> Jennifer
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rent computers. I don't know which is
> the error, any more ideas?
>
> Best,
> Jennifer
>
> ________
> De: freesurfer-boun...@nmr.mgh.harvard.edu
> en nombre de Tim Schäfer
>
> Enviado: jueves, 16 de mayo de 2019 11:50
> Para: Free
I use for my SurfStatP output p-value
> > map?
> > > > How would you do it, (tools to convert into a specific format,
> > surfaces and atlas to
> > > load on
> > > > Freeview, whic
> format, surfaces and
> > atlas to
> > > load on
> > > > Freeview, which format for those ones)?
> > > > I would be very grateful if you could detail a bit, as I am
> > new to these
> > tools!
> &
f and put together some code
that will load the Desikan data for both hemispheres and display it in
surfstat. Feel free to use it, there also is an example screenshot of the
results:
https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desikan
Best,
Tim
--
Dr. Tim Sc
rify me about this process specifically
> dura removing correction.
>
> Bests
> Faeze
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Postdoc Computa
016_20170414_T1.nii -FLAIR
> /scratch/brierm/Images/10016_20170414_FLAIR.nii -FLAIRpial -all
> -mprage -hippocampal-subfields-T1 -qcache
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Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt,
600.2 4418.1 623.8 953.8
> 155 664.6 444.3 401.5 370.4 924.9
>
>
> The above variation is because of different versions or each time
> freesurfer yields different values? Could you please educate me more on
> this. Because if the freesurfer vers
GNU/Linux
>
> recon-all -s 121202_FD49RU exited with ERRORS at Tue Jun 25 17:56:40 KST 2019
>
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr
; [0]PETSC ERROR:
> >>>> ----
> >>>> > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
> >>>> 17:29:26 CDT 2008 HG
> >>>> > revision: 4466c6289a0922d
ea whether these are just warnings and whether they affect the
FreeSurfer output or not (it seems they don't), but maybe you should still ask
the administrators of the cluster about them.
It could be that all you have to do to get rid of them is something like
module load tcsh
to ge
ure what you mean by this. Could you explain what would be the inputs
and the expected output files of this process?
If you mean that the vertex indices in the meshes of the white and your
pial-outer-smoothed surface files should match: this should be the case by
default I guess.
Best,
rre.
> Would appreciate any help.
>
> Thanks & regards
> -Korann
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gt;
> Many thanks and best regards,
>
> Lizhi
> _______
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Postdoc Computational Neuroimaging
De
; Thank you very much, Tim. Any idea for the 1st question?
>
> Thanks and best wishes,
>
> Lizhi
>
> On Sat, 13 Jul 2019 at 09:18, Tim Schäfer
> mailto:ts%2...@rcmd.org>> wrote:
> External Email - Use Caution
>
> Dear Lizhi,
>
> on your 2nd question: a
dat
> > > >>> --o mwf_FS --t1
> > > >>>
> > > >>> 2-using mri_vol2surf to extract inflated surface of MWI:
> > > >>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5
> > > >>> --interp nearest --hemi lh --o lh.inflated_MWI.w --o
10 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>应用
>
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Department of Child and Adolesce
olve this?
> If you need any information about my server, please let me know.
>
> Thank you.
> Harine.
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Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt
_
> Freesurfer mailing list
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eesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
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Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Mai
cannot just take a
random subject and read them from its ?h.aparc.a2009s.annot file: the subject
you chose may be lacking some of them. (That's why I went for fsaverage, which
was a bad idea as well.)
Tim
> On August 15, 2019 at 9:37 AM Tim Schäfer wrote:
>
>
> Ext
. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
___
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Freesurfer
me background details:-
> 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
> 2) Platform: Ubuntu 18.04.2 LTS
> 3) uname -a: Linux bodhi 4.15.0-55-generic #60-Ubuntu SMP Tue Jul 2 18:22:20
> UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>
> Many thanks
folds that don't occur in all subjects.
>
> cheers
> Bruce
> On Thu, 15 Aug 2019, Tim Schäfer
> wrote:
>
> >External Email - Use Caution
> >
> > Another interesting thing I noticed, which may be of interest to anybody
> > parsing label dat
// divide by 3 because each face participates in 3 vertices
> }
> MRIsetVoxVal(vol, vno, 0, 0, 0, volsum);
> vtxvolsum += volsum;
> }
> printf("Total vertex volume %g (mask=%d)\n", vtxvolsum, mask == NULL);
> *totvol = vtxvolsum;
>
>
w can I get this deformation
> field?
>
>
> Your help is greatly appreciated.
>
>
> Best,
> ping
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> On August 30, 2019 at 10:26 PM michele rizzi wrote:
> I put
> export SUBJECTS_DIR=
I would recommend to go through a short introduction to BASH (if that is the
shell you want to use) before working with FreeSurfer, it will save you a lot
of troub
do that same.
>
>
> Thanks
> Vasudev
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Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychos
https://github.com/dfsp-spirit/freesurferformats
Best,
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
_
> 邮箱：zhengfenglian0...@163.com
> |
>
> 签名由 网易邮箱大师 定制___
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Department of C
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Dear Eli,
could you add the command line you used and the FreeSurfer version (e.g.,
output of `cat ${FREESURFER_HOME}/VERSION`)?
Thanks,
Tim
> On September 20, 2019 at 10:14 PM "Rockers, Elijah D."
> wrote:
>
>
> External Email - Use Ca
urfer, but I do not know which files to exclude and include, so if you
have suggestions for this, it would also be very welcome. I will also look at
some public datasets to see how they did it.
[1] https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface
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You need to install the tcsh shell:
sudo apt-get install tcsh
Best,
Tim
> On October 3, 2019 at 6:30 PM Tim Schäfer wrote:
>
>
> You need to install the tcsh shell:
>
> sudo apt-get install tcsh
>
> Best,
>
; is in v6, but "IntraCranialVol" is in v5
* "Total cerebral white matter volume" is in v6, but "Total cortical white
matter volume" is in v5
Have these just been renamed, or do they carry different information? Did I
overlook anything else that changed?
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Pos
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Hi Doug,
thanks for the confirmation!
All the best,
Tim
> On October 18, 2019 at 4:01 PM "Greve, Douglas N.,Ph.D."
> wrote:
>
>
> They are just different names
>
> On 10/17/19 11:52 AM, Tim Schäfer wrote:
&g
er
>
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ring my request
>
> Sudhakar Mishra
> Research Scholar
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://surfer.nmr.mgh.harvard.edu/registration.html
> --
> Reading lh.smoothwm.asc ...
> Performing affine transform...
> Writing surface...
> -- running 'mris_convert lh.pial lh.pial.asc'
>
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You should ask that at the AFNI mailing list.
I would guess it refers to the files /mri/lh.ribbon.mgz and
/mri/rh.ribbon.mgz, but I do not know that program and that is nothing
but a wild guess.
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
t;
> I want to convert from this format to .nii format.
>
> Please help me with this.
>
> Thanks very much for considering my request
>
> Sudhakar Mishra
> Research Scholar
> ___________
> Freesurfer mailing list
> Freesurfer@nmr
ttp://bmes.cufe.edu.eg/>
> > Postdoctoral Fellow|Radiology, Harvard Medical School
> > <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550>
> > Postdoctoral Fellow| Athinoula A. Martinos Center, MGH
> > <https://www.nmr.mgh.harvard.edu/user/4550386>
> > Career Development and M
similar to Figure S1 from Bletsch et al. 2018 in tkmedit:
https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fhbm.24230&file=hbm24230-sup-0002-suppinfo02.tiff
Thanks for your time and all the best,
Tim
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Postdoc Computational Neuroimaging
Departmen
y -thickness it will read in the
> ?h.thickness file and interpret the argument as a percentage of
> thickness, which is what you want I think
>
> cheers
> Bruce
>
>
> On Thu, 12 Dec 2019, Tim Schäfer wrote:
>
> >External Email - Use Caution
> >
&g
ing/
Best,
Tim
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Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> On January 4, 2020 at 7:08 AM Frank Chau wrote:
>
>
>
have it recalculate every subject, not just those I've edited?
>
> Thank you in advance.
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>
> Dear Tim,
>
> Sorry, I am a Linux code beginner. I installed the GNU parallel in my Linux.
> May I know how to adapt the script of “ run_reconall_parallel_wrapper.bash”
> to my own need? Thank you.
>
> Regards
>
> Frank
>
>
r of the existing files)? Or
will the existing, edited files which contain a different ID be ignored during
the new run because the IDs do not match, and thus the existing edits would
have no effect?
All the best,
Tim
--
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Postdoc Computational Neuroimaging
Department of Child an
> mri_convert/mris_convert using the same file as input and output.
>
> On 1/13/2020 5:54 AM, Tim Schäfer wrote:
> > External Email - Use Caution
> >
> > Dear FreeSurfer experts,
> >
> >
> > I have two questions on subject IDs in FreeSurfer
ould be able to do something like
> mri_add_xform_to_header -c /new/path/to/xfm brain.mgz
>
> For the labels you could just use something like
> sed s/oldsubjectname/newsubjectname
>
>
>
>
> On 1/17/2020 3:48 AM, Tim Schäfer wrote:
> > External Email - Use Cauti
t know about that option
> > !
> >
> > Best,
> >
> > Tim
> >
> > > On January 21, 2020 at 4:24 PM "Greve, Douglas N.,Ph.D."
> > > wrote:
> > >
> > >
> > >
> > > For the mgz volumes, you should be able to do someth
. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
* Demo file: rawavg.mgz uploaded via FTP to /transfer/incoming/rawavg.mgz on
and the full command line
> I'll take a look. Is this the dev version you are using?
>
> cheers
> Bruce
> On Mon, 3 Feb 2020,
> Tim Schäfer wrote:
>
> >External Email - Use Caution
> >
> > Dear FreeSurfer experts,
> >
> > I am ru
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Hi Valentina,
Just to be sure I get what you are asking: do you want a visualization like
subfigure B in this image?
https://raw.githubusercontent.com/dfsp-spirit/fsbrain/master/web/fsbrain_vis_overview.jpg
So you have one value per Desikan atl
.
Maybe someone else knows an easier way?
Tim
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University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> On February 14, 2020 at 12:29
ribly efficient, but it
works. To get the direct neighbors (in distance 1) of vertex 500:
[verts, faces] = read_surf("path/to/lh.white");
mesh_neighborhood(faces, [500], 1);
Hint: beware of indexing differences (1-based in Matlab, 0-based in
C/FreeSurfer) when using it.
Tim
--
Dr. Tim
le
> or directory.
>
> I thought it might be related to permissions but running under sudo
> gives a different error. How do I fix this?
>
> - Andreas V.
> ___________
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> http
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They are all in the output folder of the subject.
The noxfix files are surfaces (in /surf/), the mgz file is a volume
(in /mri/).
Tim
> On February 25, 2020 at 4:24 AM Gabriel Tapia wrote:
>
>
> External Email - Use Caution
>
> H
-under-lubuntu/
Best,
Tim
--
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Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> On February 26, 2020 at 5:36 PM "Harrigan, T
External Email - Use Caution
Dear Frank,
if you search the log in your Dropbox for 'error', this comes up:
ERROR! FOV=284.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
Did you have a look at the orig.mgz?
Best,
downloading my orig.mgz:
> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>
> Regards
>
> Frank
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Tim Schäfer
>
> Sent: 04 March 2020 23:27
> To:
> >
> > Thanks.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.n
the T1 series will
> affect the process Recon-all? If yes, how would it impact my output results?
>
> Regards
>
> Frank
>
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Tim Schäfer
>
> Sent: 05 March 2020
> But I thought I would email this list to raise the issue. I searched the
> archives and didn’t see something similar, so maybe no one else tries to
> match those names to the LUT.
>
> ___
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> Freesurfer@nm
() function.
All the best,
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 March 23, 2020 at 12:00 PM Athanasia Mon
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I think the problem is not with running the version he downloaded, but the fact
that he could not download it, because all download links on the website at
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface are dead.
I downloaded mri_deface from th
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I am successfully running FreeView under 18.04 and 19.04, see
https://www.xsmd.org/brain/2019/06/19/freeview-libpng12-so-0-missing-under-lubuntu/
Best,
Tim
> On March 30, 2020 at 10:26 AM Koustav Chatterjee
> wrote:
>
>
> External Email
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Hi Tristan,
I'm about to setup a FreeSurfer installation on an Ubuntu system, and I
wondered whether you could elaborate on the kind of issues you are experiencing.
Best,
Tim
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Departme
bad quality images, so I feel it should be fine, but I wanted to
hear your opinion.
Best,
Tim
[1]
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimprovepialsurfaces
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychia
e in .gii format to a surface in .mgh or nii.gz
> format?
>
> I tried with mris_convert but it doesn't work.
>
>
> Best regards,
> Marina
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Hi Xiaojiang,
Given the precision of MRI scanners, I would say it's safe to assume that this
difference can be ignored.
Best,
Tim
> On April 17, 2020 at 9:02 PM Xiaojiang Yang wrote:
>
>
> External Email - Use Caution
>
> Thank
red out the issue just an hour ago. I was saving the memory and using
> int8(xyz) which restricted the values to [-128 to 127]. I was to post my
> solution.
>
> Thankyou so much
>
> Regards,
>
> Safi
>
> On Tue, Apr 21, 2020 at 4:06 PM Tim Schäfer wrote:
>
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Could you clarify what kind of meshes you are working with? Are the meshes you
are working with plane-like (parts of the pial surface), or are they closed
(e.g., generating from running marching cubes on a set of cortex voxels)?
Also what is your int
Sincerely, Fulong Xiao
>
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Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adole
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