Dear Kristine,
I am currently experimenting with prepending PreFreeSurferPipeline.sh to
recon-all (of HCP pipelines https://github.com/Washington-University/Pipelines
) which does APCP alignment, robust FOV (cropping of unrelevant parts of image
FOV - neck etc.), bias correction and (optionally
Hi Doug,
the orig looks fine and we cannot see a file orig.nofix in the subject
dirs. We still use v5.3.
But what we tried now for another similar subject was to remove falsely
labelled white matter in dura which was far away, but that fixed the
white matter errors so far inside the brain. D
On 28 February 2017 at 01:10, Francis Tyson Thomas
wrote:
>
> See utils/test/mriBuildVoronoiDiagramFloat/test-suite.log
> Please report to freesurfer@nmr.mgh.harvard.edu
>
Thanks Doug, I will give it try and update you on it.
S
--
Shane Schofield
On 26 February 2017 at 22:35:52, Douglas Greve (gr...@nmr.mgh.harvard.edu)
wrote:
Probably not. Probably you the cerebellum is still attached. You should check
the wm.mgz volume.
On 2/24/17 11:21 AM, Shane Schofield
Hi Antonin,
Thanks a lot. Those links are very helpful for me!
Cheers,
S
--
Shane Schofield
On 26 February 2017 at 12:51:23, Antonin Skoch (a...@ikem.cz) wrote:
Dear Shane,
the "topological defect" in FreeSurfer jargon means that the estimated surface
contains errors like "holes" or "handle
Hi Bruce,
Where may I find more information about the differences in recon-all or
subcortical segmentations (aseg) between 5.3 and 6.0?
Is the 6.0 pipeline still based on this paper?
Fischl, B., Salat, D. H., Busa, E., Albert, M., Dieterich, M., Haselgrove, C.,
… Dale, A. M. (2002). Whole bra
We are building up our testing infrastructure and as it currently stands
it may still be a little too catered to our specific build environment.
If freesurfer builds for you than I would skip the 'make check' stage.
The best sanity check would be to make a copy of the bert subject
folder, re-re
You can add the segmentation number of the areas you want with --segno
run it with -help to get more info
On 2/27/17 6:11 PM, Jing Gu wrote:
Dear FreeSurfer Developers,
By using the following code, we can get volume data of different areas
from
stats file.
asegstats2table --subjects N01 --
I have not see this. Can you point me to the glmdir or tar it up and
drop it to me?
On 2/27/17 4:11 PM, Tuominen, Lauri Johannes wrote:
Hi all,
Has anyone encountered a mismatch between the ocn.nii & ocn.annot
files. I'm doing a fsfast group analysis with freesurfer5.3 and the
ocn.nii file i
what are you trying to do? get mean values of thickenss in each
parcellation? If it is an annotation file, then you can use mri_segstats
with --annot. Run it with --help to get examples
On 2/27/17 8:09 PM, Julie Hall wrote:
Dear all,
I would like to use the Gordon Parcellation as segmentatio
It looks like it found something that it thinks is a DWI parameter but
isn't, and it is causing it to fail. Can you send me one of the dicoms?
In the mean time, if you
setenv FS_LOAD_DWI 0
then the error should go away
On 2/28/17 8:33 AM, Gustav Mårtensson wrote:
Hi,
I have a problem when
Hello,
I could not find any information on changing the cursor via command
line. My goal is to persistently change the default cursor style/color,
I was going to create an alias on my system.
Thanks,
Eli
Houston Methodist. Leading Medicine.
U.S. News & World Report has recognized Houston Method
Hi Eli,
There is no command-line option to change the default cursor
style/color. However, if you change it from the GUI, the change will be
saved when you close freeview so it will be the default one the next
time you open freeview.
Best,
Ruopeng
On 02/28/2017 11:35 AM, Rockers, Elijah D. wr
Hi,
I was able to apply the morph using combined_toColin27_elreg_aseg.tm3d instead
of fullCSVmorph.tm3d.
The resulting coordinates are wrong, but it proves that memory is not an issue
- combined_toColin27_elreg_aseg.tm3d is 458MB, while fullCVSmorph.tm3d is only
50Mb.
So what else can be the
Hi Cristian,
Can you upload your files for us?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Lilla
On Tue, 28 Feb 2017, Donos, Cristian wrote:
Hi,
I was able to apply the morph using combined_toColin27_elreg_aseg.tm3d instead
of fullCSVmorph.tm3d.
The resulting coordinates are wrong, but it
Hello Freesurfer,
I have couple questions.
1) If I have 2 commands (e.g., mri_normalize -a 30 and mris_inflate -n 30)
and I want recon-all to execute both commands. Should I create 2 different
expert opts files or 1 expert opts file with both commands in it? Also, how
do I include the expert flag w
I'm using the Freesurfer output to register my DWI images to, on which I would
like to apply graph theory on
(Sorry I'm a newbie in imaging so let me know if this is not the answer you're
looking for)
Sent from phone
Please excuse shortness or typographical errors
On 01 Mar 2017, at 02:42,
Dear experts,
I would like to create modified aparc.a2009s+aseg file with relevant parts of
parahippocampal cortical ribbon voxel labels replaced by labels derived from
surface labels of entorhinal and parahippocampal cortex (created also by
default in recon-all). This modified aparc.a2009s+ase
Dear Paul,
1) You find pretty thoroughful info on expert options file here:
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences
2) recon-all -autorecon2-cp -autorecon3 is ok (btw -autorecon2-cp and
-autorecon2-wm runs the same commands, at least in version 6.0).
3) There is in
Hi all !
I would like to convert my files : volumetrics nifti files to surfaces
files.
My volumetrics nifti files come from an Atlas and I would like to convert
them to surfaces files (i need the surfaces files).
Could you please tell me the process because I have tried many things like :
mri_vo
Dear Freesurfer experts,
I am new to using freesurfer and was wondering if anyone could explain to me
the difference in output generated by BrainSegVolNotVent and
BrainSegVolNotVentSurf. I am aware that BrainSegVolNotVent refers to the
Brain Segmentation Volume Without Ventricles and BrainSegVo
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