Dear Douglas,
thank you for the file and response. This new cluster-sess file works OK.
Antonin
_
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
To: Antonin Skoch [mailto:a...@medicon.cz], Freesurfer@nmr.mgh.harvard.edu
[mailto:Freesurfer@nmr.mgh.harvard.edu]
Sent: Tue, 03
) dimension.
Simple modification of the code like
if (size(rho1.vol,4)==1)
rho1mn.vol= rho1.vol
else
rho1mn.vol = mean(rho1.vol,4);
end
solved the problem in my case.
Regards,
Antonin Skoch
Institute for Clinical and Experimental Medicine
National Institute for Mental Health
Czech
ruction of pial
surface works as expected (i.e. reflecting both brainmask edit and FLAIRpial
refinement).
Is this bug or expected behavior? Or are we doing something wrong?
Regards,
Antonin Skoch
MR Unit
Institute for Clinical and Experimental Medicine
Czec
Dear FreeSurfer experts,
we are using FLAIR images to improve pial surface detection. In many cases this
works OK, however, in some cases this procedure fails and the corrected pial
surfaces are much worse than before.
I uploaded 2 example subjects FLAIRpial_OK and FLAIRpial_not_OK to
ftp://s
Dear FreeSurfer experts,
could you please look at the issue mentioned below? I did not receive any
answer to my post, probably it got lost unattended.
Antonin Skoch
_
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
To: Antonin Skoch [mailto:a...@medicon.cz]
Cc: Nick Schmansky
Dear FreeSurfer experts,
I came across failure in mni152reg script. It is related to the fact that my
MNI152 template is installed (via neurodebian package of ubuntu) to the
directory where normal user does not have write permissions (see log file in
the attachment).
I expect that this could be
...@nmr.mgh.harvard.edu], Antonin Skoch
[mailto:a...@medicon.cz]
Sent: Wed, 13 May 2015 16:39:26 +0100
Subject: Re: [Freesurfer] FLAIRpial correction fails in some cases
Hello Antonin,
Please try processing your subject with the dev version of freesurfer as
it may fix the issue you are encountering. It can be
, but I did not grasp how it is decided
which steps to run and which not. When -make directive is not specified the
make tools are not used for that, are they?
Regards,
Antonin
_
From: Nick Schmansky, MGH [mailto:ni...@nmr.mgh.harvard.edu]
To: Antonin Skoch [mailto:a...@medicon.cz], Bruce
Dear FreeSurfer experts,
when inspecting my reconstructions I sometimes encounter the problem with white
surface estimation extending outside brain to outer non-brain structures. This
is evident from coregistered FLAIR images where low signal is present in these
areas.
In these cases FLAIRpial
Dear Kalyan,
do you use standard pial surface reconstruction via T1 images, or optional pial
surface refinement with T2/FLAIR images?
I had similar problems with FLAIRpial surface refinement. The corrected pial
surface appeared jagged and some areas were artificially cut out (whereas they
were
Dear experts,
I came several times across the situation when pial surface from one hemisphere
is crossing the surface of other hemishpere (see the attached screenshot). Is
there any way how to correct for this error?
Regards,
Antonin Skoch___
Freesur
Dear experts,
is here any way how to improve white surface estimation in situations when this
surface "leaks" from the brain to the outer non-brain structures? (See the
attached screenshot).
This problem consequently affects pial surface estimation, which is not
correctable by FLAIRpial correct
Dear Bruce,
the subject with overlapping reconstructed pial surfaces is uploaded to
surfer.nmr.mgh.harvard.edu/pub/transfer/incoming/20150727_overlap_hemispheres.tar.gz
The problem appears at coronal slices 46-54. Thank you very much for your help.
Regards,
Antonin Skoch__
Dear experts,
during the manual correction of freesurfer reconstruction I encountered
following problem:
White surface did not follow gray / white matter boundary probably partly due
to skullstrip error and partly to the insufficient local gray/white matter
contrast. I tried to fix it by editi
,
Antonin Skoch
_
hmmm, that could be a problem, although the surfaces look pretty good, so
maybe not. Try V6 beta and see if it still happens. Or upload the subject
and we will try it out
cheers
Bruce
On Fri, 19 Jun 2015, Antonin Skoch wrote:
> Dear FreeSur
e orig that means
> it was an incorrectly fixed topological defect that you need to manually
> correct. I'll see if we can find someone here to take a look.
> Bruce
On Wed, 29 Jul
2015, Antonin Skoch wrote:
> Dear experts,
>
> during the ma
as at righ hemispheres at the
convexity
I see the same behavior in freesurfer 5.3. and in v6 beta version.
Is this a bug in mris_make_surfaces or can it happen normally in some cases?
How can I fix this problem?
Regards,
Antonin Skoch
> Dear Bruce,> no, both ?h.orig.nofix and ?h.orig are o
system
before the error is issued.
Regards,
Antonin Skoch
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Dear experts,
I am potentially also interested in correct using of -T2pial feature with
longitudinal stream.
The first (standard cross-sectional) and third step (-long ) was already
elaborated here, but I am, however, not sure how to process by T2pial in the
second step ( -base), which crea
correct?
Regards,
Antonin Skoch
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addressed. If you
.
Regards,
Antonin Skoch
using T2 threshold of 2.00 sigmas above the mean (default=2)
using T2 threshold of 3.00 sigmas below the mean (default=2)
using filled.hires as filled name
using wm.hires as filled name
reading original vertex positions from white.deformed
reading previously compute gray/white
---
Hi Antonin
I'm having trouble parsing your image. Could you:1. Send the voxel coords of
the location that you see overlap.
2. Send an image with *only* the two overlapping surfaces on, shown in
different colors? thanks
Bruce
On Fri, 18 Nov 2016, Antonin Skoch wrote:
step?
Regards,
Antonin Skoch
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addressed. If you
parameters).
Best, Martin
> On Nov 14, 2016, at 10:17 PM, Antonin Skoch wrote:
>
> Dear experts,
>
> I am trying to understand how the pial and white surfaces are generated in
> longitudinal stream using information from the reconstructed base template
> (freeSurfe
surfaceRAS
talairached surfaceRAS to surfaceRAS
Volume Geometry vox2ras
Volume Geometry vox2ras-tkr
Antonin
From: Bruce Fischl
To: Antonin Skoch
Sent: 11/23/2016 12:42 AM
Subject: Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement
-issue with overlapping pial surfaces
this.
Regards,
Antonin
yes, all the surfaces used by mris_make_surface must share things like
ras2vox and such
cheers and happy thanksgiving
Brue
On Wed, 23 Nov 2016, Antonin Skoch wrote:
> Bruce,
>
> and do you require that also all volumes which are passed as arg
Dear experts,
given sub-optimal results of my surfaces I referred to in my previous post, I
have tested several different settings and input data preparation to obtain
optimal pial surfaces in my modified HCP pipeline. I tested all variants in 5
representative subjects.
My modified HCP pipelin
tions when the images are
very differently aligned, the --init-fsl totally fails.
Is it possible to realize it by supplying both --init-reg and --init-coreg (or
even combination of --init-reg --init-best to try both mri_coreg and flirt)?
Regards,
Ant
does my_initial_lta.lta have the subject name in it? If not, then put
that argument before the --s
On 12/05/2016 10:34 AM, Antonin Skoch wrote:
> Dear experts,
>
> I am having trouble using --init-reg option in b
attachments. They are included in
the original mail.
Best regards and merry Christmas,
Antonin Skoch
From: Antonin Skoch
To:
Sent: 12/21/2016 1:41 AM
Subject: pial surface errors - V6beta
Dear experts,
in my data I quite often encounter errors in pial surface which is probably
, how to correct this error?
My second question, is it possible to check non-linear Talairach registration,
i.e. talairach.m3z?
Regards,
Antonin Skoch
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behavior also for V6 version
of freeview?
Regards,
Antonin Skoch
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The information in this e-mail is intended only for the person to
in freeview have been
used. What do you think?
4.
Do you think there is a chance to implement recon-all to preserve part of the
surface which has been repositioned by this tool in case of recon-all rerun
(similarly like it is done with other edits)?
Regards,
Antonin Skoch
Dear Paul,
you can also try to play with "reposition surface" tool in freeview, where you
(apart from other options) can directly edit coordinates of the surface
vertices.
However, this tool is not well documented and I myself would like to know the
significance of some of the parameters - see
Dear Paul,
I could chime in with my current limited experiences with this tool (using
V6beta version of freeview). Maybe they could be helpful for you.
Most straigthforward is using "edit coordinate":
Select the surface you want to edit.
Select tools-reposition surface - edit coordinate.
With s
do appreciate it. Do I need to insert a
vertex number or just the coordinates? Because when i clicked on the
surface outside the pial (see screenshot) the vertex = N/A ( see
screenshot). ALso, what step of recon-all should i start? (autorecon-2 or
autorecon3)?
Best,
PaulOn Tue, Jan 10, 2017 at 3:
Dear Paul,
I am quite surprised that you were successful to estimate correct GM/WM
boundary using this tool. As far as I know and looking at the source code, this
tool GLOBALLY moves the position of the specified surface to some amount, so it
cannot be used to correct local errors. It is used e
ts). Thank you.
Best,
PaulOn Wed, Jan 11, 2017 at 12:32 PM, Antonin Skoch wrote:
> Dear Paul,
>
> I am quite surprised that you were successful to estimate correct GM/WM
> boundary using this tool. As far as I know and looking at the source code,
> this tool GLOBALLY moves the p
what resolution was your input images, and whether you
used additional high-resolution T2. The effect of various image resolution on
the reliability of results is also well discussed in above-mentioned paper I
think.
Regards,
Antonin Skoch
comment on how to optimally handle such situations?
Regards,
Antonin Skoch
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The information in this e-mail is intended only for the
volume, just edit
the long."
So for your ventricle correction, you could either clean up the cross data and
hope it caries over to the long (it should), or directly edit the long aseg.
Best, Martin
> On 16 Jan 2017, at 23:23, Antonin Skoch wrote:
>
> Dear experts,
>
> I a
seg.auto of -long differs
> (they do not have the same input) which is undesirable. So I think I do not
> have any other option than to edit aseg.presurf in -long again.
>
> Could you please comment on how to optimally handle such situations?
>
> Regards,
>
> Antonin
Dear Ruopeng,
I have the same problem with missing toolbars in freeView, however I am not
successful with command
defaults delete edu.harvard.mgh.nmr.FreeView
The command shows:
defaults delete: couldn't remove non-existent domain
edu.harvard.mgh.nmr.FreeView
My command
defaults domains
Dear Ruopeng,
I am using Ubuntu 12.04. LTS 32bits.
There is no directory
~/Library/Preferences
in my home directory. There is only "GNUstep" directory containing
subdirectories "Defaults" and "Library". "Library" dir is empty and "Defaults"
contains .GNUstepDefaults file, which is very short
Dear Ruopeng,
thank you, it worked! Only, just to let you know, this tiny popup menu item was
completely blank in my case, without any inscription. When I left-clicked at
it, the menu bar appeared, and on this popup menu item only checkmark newly
appeared.
Regards,
Antonin
Dear FreeSurfer experts,
during inspection of reconstructions of our data, I found that in many cases
the pial (and sometimes also white) surface is extending out of the brain and
encircling the optical chiasm. Does this situation has any effect to the
results (i.e. cortex parcellation, whole-b
Dear experts,
I am sending the example subject named chiasma_question.tar.gz to your FTP
server.
The issue with encircling chiasma is located in slices ~134-140.
According to Aparc.a2009s+aseg the tissue is marked as optical chiasm, but also
part of it is labeled as left cerebral white matter.
Dear FreeSurfer experts,
I am getting the same error with malloc(): memory corruption on mri_segstats
invoked within mri_glmfit-sim. Apart from Frances, the process continues
forever without any output after error message (i.e. without "Writing to..."
and "Abort..." line).
My commandline is:
there an actual table of reconstruction steps for 5.3.2 version?
Regards,
Antonin Skoch
Institute for Clinical and Experimental Medicine
Prague, Czech Republic
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very much in advance for clarification,
Antonin Skoch
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The information in this e-mail is intended only for the person to whom it is
to cluster size values in .csd files?
Thank you in advance for help.
Regards,
Antonin Skoch
> Dear FreeSurfer experts,
>
> I am using mri_surfcluster to compare results from PALM and FreeSurfer
> cluster extent inference.
>
> I came across several issues in mri_surfcluster
hese
values do not correspond to area of real lh.white vertices.
Thank you for your kind support.
Regards,
Antonin Skoch
It is quite confusing and took us some time to understand ourselves.
When we create an average subject like fsaverage, we have to create a
triangular mesh just like we do
could significantly reduce time
spent on edits. Does it make sense?
Regards,
Antonin Skoch
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The information in this e-mail is
-linear deformations in some of the fast progressing
brains.
Best, Martin
> On 23 Jan 2017, at 23:11, Antonin Skoch wrote:
>
> Dear experts,
>
> I am currently starting longitudinal analysis of data I previously corrected
> in cross-sectional stream (FreeSurfer v5.3).
> T
registration will not be run again.
And, also, if you do T2 or FLAIR adjustment of surfaces, it could be maybe
beneficial to add -clean-T2 (-clean-FLAIR) to reinvoke T2/FLAIR registration to
T1. There is new implementation of initial registration method (mri_coreg) for
bbregister.
Regards,
Antonin Skoch
have been fixed and some tools improved), but definitelly it would require to
re-inspect your data after reprocessing.
Antonin Skoch
Dear experts,
Does anybody could answer my last request ?Best,
Matthieu
2017-01-26 9:58 GMT+01:00 Matthieu Vanhoutte :
> Dear FS's experts,
>
>
dinalEdits#RerunningEditsCommands
Regards,
Antonin Skoch
Hello,
After I make edits to my aseg output in the longitudinal stream, do I just
run the following command to recreate the final volumes:recon-long
-autorecon2-noaseg -subjid
I assume the -subjid is the name of the edited time point and is
t
Dear Paul,
maybe this is implicit, but to assure:
you have also to include -autorecon3.
Therefore the full command is:
recon-all -s subject_id -autorecon2-cp -autorecon3 -T2pial
Antonin
Yes, I think so
> On Feb 5, 2017, at 2:47 PM, miracoo...@gmail.com wrote:
>
> Hello,
> I ran the entire
eline"
# Input Variables
SubjectID="$1"
SubjectDIR="$2"
T1wImage="$3" #T1 FreeSurfer Input
T2wImage="$4" #T2 FreeSurfer Input
recon-all -s $SubjectID -autorecon-all -i "$T1wImage"_T1.nii -T2
"$T2wImage"_T2.nii -T2pial -parallel -hires
heers
Bruce
On Tue, 7
Feb 2017, Antonin Skoch wrote:
> Dear experts,
>
> I have reprocessed my groups of subjects (originally processed by v5.3) by
> v6.0. I am using -FLAIRpial for pial surface refinement.
>
> I have noticed that the pial surfaces in v6.0 after -FLAIRpial are
, thank you for your feedback.
Antonin
Since I believe you said you are using my code, I would recommend to stick
with 5.3 at this time.Peace,
Matt.
From: on behalf of Antonin Skoch
Reply-To: Freesurfer support list
Date: Tuesday, February 7, 2017 at 2:59 PM
To:
Subject: Re: [Freesurfer
Dear Graham,
you could also try mrconvert of mrtrix3. This tool is very useful and has very
good support.
http://mrtrix.readthedocs.io/en/latest/reference/commands/mrconvert.html
community.mrtrix.org
Regards,
Antonin
Unfortunately I'm not allowed to share these files without direct IRB appro
Dear Chris,
I have found that -n 15 is for our 0.7x0.7x0.7mm3 data not enough.
I determined optimal value -n 30, empirically, by looking at the shape of
inflated surface with various number of iterations. Over -n 30 there was almost
no further progression in inflation.
I suppose that better m
---
> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.
> harvard.edu]" im Auftrag von "Antonin Skoch [a...@ikem.cz]
> *Gesendet:* Donnerstag, 9. Februar 2017 16:20
> *An:* freesurfer@nmr.mgh.harvard.edu
> *Betreff:* Re: [Freesurfer] Expert
Dear Zhewei,
I think that the problem you report is caused by the fact, that .mat file from
FLIRT codes vox2vox transformation, so that cannot be applied to another
dataset (in your case fMRI) unless it has the same geometry as the original
image the .mat file was generated on.
Antonin
Can
/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
where aparc replace by name of your generated Yeo atlas annot file.
Regards,
Antonin Skoch
Hi everyone,
I was wondering if someone could please address the following question
regarding FreeSurfer usage.I would really appreciate any
Hi,
could not be the issue python version mismatch? tractstats2table is python
script, maybe there is a problem.
Antonin
Hi Adarsh – What operating system are you running this on? It runs fine for me
with this input file when I test it on both a mac and a linux computer.a.y
From:
mailto:fr
Dear Experts,
according to the log, Vasudev is using version 5.3-HCP. Therefore I expect that
he is running FreeSurfer inside HCP pipeline scripts. The problem is that the
use of 6.0 version with HCP pipeline scripts is not currently recommended.
see
http://www.mail-archive.com/freesurfer@nmr.
something higher.
Or you can try dev version of freeSurfer and experiment with explicit setting
of T2 intensity threshold using -T2_min and -T2_outside_min parameters.
Regards,
Antonin Skoch
You could try with the HCP Pipelines and see if that helps:
https://github.com/Washington-University
freeSurfer git repository to external users?
Regards,
Antonin Skoch
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Dear Shane,
use this command:
mri_segstats --annot my_subject_id lh aparc --i
$SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
Look at the info on FreeSurfer wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/LGI
Antonin Skoch
Hi Freesurfer,
How can I get the LGI
Dear Vasudev,
on what filesystem does your working directory reside?
According to the path to your data it seems that you use some external drive,
probably with non-unix-like filesystem.
The error most probably means, that your filesystem does not support symbolic
links.
Regards,
Antonin
Dea
Dear Doug,
I was wondering, why do you prefer mni152reg to mri_coreg for gregistration to
MNI? According to help, mri_coreg is also able to do 12 DOF registration.
Antonin
mri_coreg is the FS implementation of spm_coreg (spmregister) both of which
use normalized mutual info. bbregister uses
much more severe, spanning not only the
blue encircled region.
I would very appreciate your expert opinion on this.
Regards,
Antonin Skoch
Announcing the official release of Mindboggle (http://mindboggle.info),
open source software <http://mindboggle.info/software.html> and data
nspect brainmask.mgz or wm.mgz
and correct errors.
You can also find more information on the forum, there are quite large amount
of posts related to topological defects.
For example:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30763.html
Antonin Skoch
Hi Freesurfer Te
Dear Paul,
LTA means transformation matrix stored in .lta format.
This matrix can encode transformation between various coordinate spaces.
What coordinate systems transform this .lta from and to is specified by string
in the .lta file. Typically this type could be vox2RAS, RAS2vox, vox2vox or
y 10 smartphone.
From: Antonin Skoch
Sent: Sunday, February 26, 2017 3:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] Fw: PETsurfer mri_coreg problem
Dear Paul,
LTA means transformation matrix stored in .lta format.
This ma
/HippocampalSubfields
This should be more precise than "standard" aseg segmentation and given you
have also 3D T2, multispectral T1 and T2 segmentation can be used.
Antonin Skoch
Dear Shane,
I have checked the aseg.mgz and in only one I would say the segmentation failed
however the others look fi
d.edu
namens Antonin Skoch
Verzonden: maandag 27 februari 2017 12:31
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus
Dear Michel,
Given your resolution 0.8x0.8x0.8, did you run recon-all with -hires flag? What
did you used T2 image for? As a -T
namens Antonin Skoch
Verzonden: maandag 27 februari 2017 13:27
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Overestimation of volume in Hippocampus
Dear Michel,
by default in the recon-all the input images are resampled to 1x1x1mm3. To
disable this and retain your resolution
2 reg. It might (probably does) work
fine. On 2/25/17 5:33 PM, Antonin Skoch wrote:
Dear Doug,
I was wondering, why do you prefer mni152reg to mri_coreg for gregistration to
MNI? According to help, mri_coreg is also able to do 12 DOF registration.
Antonin
mri_coreg is the FS implementati
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
recent build of dev version of Freesurfer from 28/2/2017.
Could you suggest where could be the problem?
Or could you advice different, possibly more simple way, how to achieve my goal?
Thank you in advance.
Regards,
Antonin Skoch
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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
you in advance for clarification.
Regards,
Antonin Skoch
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Try adding --no-unknown to the label2annot command line
On 02/28/2017 04:45 PM, Antonin Skoch wrote:
> 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
, Antonin Skoch wrote:
> Dear Doug,
>
> thank you, adding --no-unknown indeed fixed the global shuffling of
> the label names. However, last line of .ctab seems not to be read this
> time and produced .annot does not contain perirhinal label.
>
> My modified .ctab file lo
Dear Randy,
from the log file you provided it seems that both of your jobs exited on the
insufficient RAM. You should check your available RAM resources.
brainstem-structures:
std::bad_alloc
hippocampal subfiels:
Out of memory.
Regards,
Antonin
Hello FreeSurfer Experts/Community,
I a
Dear Mel,
if your recon in 5.3 version finished without error, there must be files
lh.orig.nofix and rh.orig.nofix present in the subj_id/surf directory.
This type of error is most frequently due to incorrectly fixed topological
defect. The original wm.mgz and orig.nofix errors can be quite a la
Dear Paul,
I suppose the clue is following messages from your recon-all.log file:
FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
and
cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s
/opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
ln: failed to create symb
Thanks Antonin. Also, I got this error.log file in my label folder. Do you
think it is due to the slash problem?
Best,
PaulOn Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch wrote:
> Dear Paul,
>
> I suppose the clue is following messages from your recon-all.log file:
>
> FREESURFER_HOME
Dear Eli,
I have looked at your data.
Due to the fact that the white matter does have intensity well below 110 in the
large portion of white matter area under your problematic spot, I think that
instead of editing wm.mgz the better way in your case would be to add some
control points to the wh
2017 at 5:41 PM, Antonin Skoch wrote:
> Dear Paul,
>
> the slash problem prevents to properly create symbolic link to fsaverage in
> your SUBJECTS_DIR.
>
> Then, the mri_label2label could not find the fsaverage label file since
> symbolic link for fsaverage does not exist, h
e non-overlaping entorhinal and perirhinal labels for the
purpose of generating custom aparc+aseg from them?
Regards,
Antonin Skoch
Dear experts,
Could you please provide me the information how exactly the
*_exvivo.thresh.labels have been thresholded?According to this post,
http://www.mail-archiv
Dear Daniel,
For the "outer" boundary of your ROI, I would try the betsurf from FSL for the
inner skull surface estimation. This should be more precise than using
brainmask.mgz.
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide
Antonin
You could remove the brain (as found in aseg.mgz) from
surf fsaverage lh --i labelseg.mgh --id 1 --l
newlabel1.label
On 03/02/2017 12:05 PM, Antonin Skoch wrote:
> Dear Doug,
>
> I am using quite recent dev version built 8/2/2017.
>
> mris_label2annot of this version is following:
>
> $Id: mris_label2annot.c,v 1.20 2016/01/07 2
Dear Martin,
I think yes, you can use PALM with FreeSurfer surfaces, see my conversation
with Anderson on FSL list:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=239088
but beware not to forget to include average the vertex ar
Dear Eli,
did you read my response to your previous thread?
I recommended you to try adding control points to the white matter.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51959.html
Regards,
Antonin
Hello all,
Again, I tried to modify the white matter surface by adding vox
urfer, so would it be possible for you
> to share detailed step-by-step guide and PALM command after I run mri_glmfit
> command and how and where to include '?h.white.avg.area.mgh' file?
>
> I would really appreciate any help.
>
> On Mon, Mar 6, 2017 at 4:28 PM, Antonin Skoch
ne 81)
palm_core(varargin{:});
Could you please help me in resolving this error?
Thanks much.
On Tue, Mar 7, 2017 at 2:55 PM, Antonin Skoch wrote:
> Dear Martin,
>
> input -i input file is
>
> lh.MEQ_LGI.10.mgh file in your glmdir directory (for left hemisphere).
>
> As y
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