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
On Tue, Mar 7, 2017 at 3:48 PM, Antonin Skoch wrote:
> Dear Martin,
>
> after -s option, there have to be 2 arguments, as I specified in my previous
> mail:
>
> -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh
>
> And beware that -C has to have negative
community forum, they are usually
responding very quickly and each post gives detailed attention.
Regards,
Antonin Skoch
??Dear Tracula experts,
I am applying Tracula on a longitudinal data set, and have some questions I am
hoping you could help me with:
Firstly, upon visual inspection, several
y little to add :-)
>>>
>>> Only a few suggestions:
>>>
>>> - With surfaces, both cluster and TFCE statistics tend to be slow.
>>> Consider using the tail approximation ("-approx tail -n 500
>>> -nouncorrected")
>>>
>>&
ot Antonin.
Sahil
On Wed, Mar 8, 2017 at 2:06 PM, Antonin Skoch wrote:
> Dear Sahil,
>
> could you send the full command-line and unthresholded view of
> *_clustere_tstat_fwep ?
>
> How the data showed in screenshot 1 were produced?
>
> How are the a
to thickness, volume and area maps?
Thanks you so much Antonin for all your help.
Sahil
On Wed, Mar 8, 2017 at 3:05 PM, Antonin Skoch wrote:
> Dear Sahil,
>
> If you used -logp as Anderson suggested, you should set your min to 1.3 to
> threshold your *_clustere_tstat_fwep map and s
the data and the detailed commands I am using to run the analysis?
Thanks a lot,
Sahil
On Wed, Mar 8, 2017 at 11:54 PM, Antonin Skoch wrote:
> Dear Sahil,
>
> to assure that there is no other issue with your setup, I would recommend to
> obtain cluster-wise p-pvalue of that
ng at
the data and the detailed commands I am using to run the analysis?
Thanks a lot,
Sahil
On Wed, Mar 8, 2017 at 11:54 PM, Antonin Skoch wrote:
> Dear Sahil,
>
> to assure that there is no other issue with your setup, I would recommend to
> obtain cluster-wise p
Thanks a lot for Antonin,
Sahil
On Fri, Mar 10, 2017 at 1:58 AM, Antonin Skoch wrote:
> Dear Sahil,
>
> thinking of that, the comparisons I suggested in previous mail are
> probably valid only for the case of orthogonal design. And even with the
> orthogonal design
advise how to diagnose and solve the error?
I am using development version from beginning of february 2017.
Regards,
Antonin Skoch
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The
ons due to the different input used.
Regards,
Antonin Skoch
Hi Bruce,
I don¹t think the hires T1w and T2w stuff are as accurate as 5.3 in the
HCP 0.7mm data that I have looked at (and as I recall at least one other
user had some similar issues, as did one of my collaborators), but that
was a
!
Regards,
Antonin
Hi Antonin, can you upload that subject? In one case using 700um, the white
surface looked fine, and I did not see much of a difference with the 1mm scan.
On 3/14/17 5:39 AM, Antonin Skoch wrote:
Dear experts,
can also be the difference between v5.3 and v6.0 behavior in HCP
Dear David,
did you use
-uselongbasewmedits
in your recon-all -long run?
If this flag is not used, the wm edits are transfered to long from cross, not
from the base.
Regards,
Antonin Skoch
Andrew, thanks for your response. I am still not seeing the white matter edit
performance that I
. Could you please comment
on?
Regards,
Antonin Skoch
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The information in this e-mail is intended only for the person to whom it is
= (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix)
by
set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix)
Antonin Skoch
Hello FreeSurfer Developers, I have installed Freesurfer on Windows using
VMware - CentOS 64-bit (the one from FSLuser Linux installation).
Everytime I
50,60,70, and
80,90,100, the option would be:
-s 50 60 70 -s 80 90 100
Regards,
Antonin Skoch
Hello FreeSurfer Community,
I am attempting to use mri_watershed to create BEM surfaces, but for some of my
subjects part of the cerebellum is being cut off. Adjusting the threshold was
not sufficient
the edits are not overwritten in case of new recon-all
rerun.
Maybe other experts could comment on my workaround approach, it would also help
me out.
Regards,
Antonin Skoch
I believe what I am seeing in the long stream is the edits not properly taking
effect.I uploaded a subject with two
rns symbolic links, too. Is there any way I could make it work on this
> virtual machine? I coud try to substitute all ln commands with cp or
> something like that.
>
> Thanks.
>
> Patricia
>
> 2017-04-04 13:43 GMT+02:00 Antonin Skoch :
>
>> Dear Pa
?
Regards,
Antonin Skoch
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e
documentation is more close to the optimum
(the three steps: normalization, mask and segmentation steps are run only when
it is needed - in -autorecon2-cp, not in -autorecon2-wm).
Antonin
I think the stages in the command line help are out of date
On 04/08/2017 05:58 PM, Antonin Skoch wrote
corrupted pixels. Note new oblique strips.
This is not only display issue. The mri_diff 001.mgz 001_2.mgz outputs:
diffcount 287447
Volumes differ in pixel data
maxdiff 966. at 171 255 30 0
I am using recent development version of freesurfer from 04/2017.
Regards,
Ant
/PialEdits_freeview
Antonin Skoch
Hi David,
Thank you for the feedback! I followed your advice's and everything has been
resolved. Highly appreciated!Cheers,
John
Sent with [ProtonMail](https://protonmail.com) Secure Email.
Original Message
Subject: Re: [Freesurfer] manual edits
Local
?h.white to directly follow
edits of wm.mgz
As for editing of 001.mgz, beware the pitfall with editing images with mutually
different geometry in FreeView I posted today:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52729.html
Antonin Skoch
Dear All,
Regarding wm.mgz edits
edit volumes in their local space. I didn't
find any screenshots in your last email but my guess is the oblique strip is
due to nearest neighbor resampling. You can choose "-trilinear" or "-cubic" in
the command line when you load the images. Best,
Ruopeng
On 04/
Dear Shane,
could you please post screenshots of ?h.orig.nofix and ?h.orig in the
problematic regions?
Antonin Skoch
Hello Freesurfer Team,
I am trying to recover thin WM strands in the temporal lobe by using control
points but to no avail (screenshot)
Any suggestions please? These
s like wlo could also help depending on how wrong the normalization is.
Upload a subject and I'll take a look cheers
Bruce
On Thu, 20 Apr 2017, Antonin Skoch wrote: Dear David,
thank you for the feedback; I saw your posts concerning edits and responded
to them, see
http://www.mail-archive
interpolation could have such profound effect !
I will try your suggestions and let you know.
Antonin
From: Bruce Fischl
To: Antonin Skoch
Cc:
Sent: 4/21/2017 1:00 AM
Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM
basically be a best-guiess of where these nuclei might be,
with no scope for subject-specific refinement).
Antonin Skoch
Hi al, Just wondering if anyone has any suggestionsto my previous question
as to why the volume from mni152 space would be rotated, even though the
MNI152 to subject T1 alignment
slice number?
On 04/24/2017 11:16 AM, Douglas N Greve wrote:
> Anonin, of the three subjects you sent, which one is shown in these
> pictures?
>
>
> On 04/19/2017 05:23 PM, Antonin Skoch wrote:
>> Dear experts,
>>
>> I am sending just one more example to illust
Dear fwd9707,
see these threads:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52560.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html
Antonin Skoch
Dear all
I performed the recon all in virtualbox (with centos 7), and there
error
that to me?
On 04/24/2017 12:49 PM, Antonin Skoch wrote:
> Dear Doug,
>
> the subject with leak of white surface outside brain (my first post with
> screenshots) is subject 1. Slice number (coronal) around 100.
> The subject in second post (with text below) is subject 2, slice num
again on my side.
Antonin
It is subject #1, trying to replicate in our version of 5.3 using the
scripts/recon-all.local-copy ./recon-all.local-copy -all -FLAIRpial -s
1.dng.v53.local-cubic -cubicThe results were close, but they were not exact
On 5/1/17 4:13 PM, Antonin Skoch wrote:
Dear Doug
>0 and <1; larger values would correspond to cleaner
skull-strip but higher chance of brain erosion. Default is set
conservatively at 0.40, which provide approx. the same
negligible level of brain erosion as 'mri_watershed'.
Antonin
-all.local-copy ./recon-all.local-copy -all -FLAIRpial -s
1.dng.v53.local-cubic -cubicThe results were close, but they were not exact
On 5/1/17 4:13 PM, Antonin Skoch wrote:
Dear Doug,
that is strange. What precisely you cannot replicate? The results with v5.3 or
with v6.0? What subject from the
of your
results, you probably would need to re-inspect your data again and correct
newly appeared errors in surfaces.
Antonin Skoch
all the edits will be taken into account regardless of what command line args
you use On 6/9/17 3:08 AM, Manuel Delgado wrote:
Dear all,
Regarding this issue
analysis? Could you please comment on what tools
inside FreeSurfer framework can be used for this purpose? What is your common
aproach to find regression model which best approximates the relation present
in the data?
Thank you in advance for pointing me to right direction.
Regards,
Antonin
for some situations/datasets?
Antonin Skoch
Hello FreeSurfer Developers,
I am attempting to switch the Desikan-Killiany atlas of FreeSurfer to Civet.
But I have no idea to solve the problem. Would you like to give me some
suggestions or some detailed steps to help me accomplish the tasks
differently.
This paper might offer some
insights.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408913/
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Fri, Jul 14, 2017 at 8:29 AM, Antonin Skoch wrote:
> Dear Zhiquiang,
>
> as a regula
is only present in coronal view. Looking at the data in 3D
display, I see nothing unusual except that the density of the vertices in that
region is very low. Is it only an issue with freeView display?
Regards,
Antonin Skoch
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u/pub/dist/freesurfer/dev/freesurfer-Linux-centos6_x86_64-dev.tar.gz
How is the build of dev version sheduled?
Antonin Skoch
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The information
Dear experts,
I would like to ask, whether I could obtain a basic general info on samseg
routines - what specifically are they doing (publication reference) and how to
use them?
Regards,
Antonin Skoch
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Dear Clemens,
this is very strange, since the talairach.xfm is not by default overwritten in
recon-all (unless you specified -clean-tal to recon-all).
When you rerun your recon-all after modifying talairach.xfm, your automatic
talairach registration will be saved into talairach.auto.xfm, theref
Dear Elizabeth,
I would guess that something went seriously wrong in the recon-all with your
data. Does Talairach registration and skull strip look reasonable?
Antonin Skoch
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https
Dear Clemens,
I am almost out of ideas, since the behaviour is contrary to my expectations.
I would expect that if you run your recon by
recon-all -s subject_id -all
the files you named
before_recon-all_talairach.xfm and after_recon-all_alairach.xfm
should be identical.
Could you assure th
-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Clemens
-freesurfer-boun...@nmr.mgh.harvard.edu schrieb: -
An: freesurfer@nmr.mgh.harvard.edu
Von: Antonin Skoch
Gesendet von: freesurfer-boun...@nmr.mgh.harvard.edu
Datum: 16.08.2017 12:23
Betreff: Re: [Freesurfer] Antwort: Re: use manually
Dear Bruce, Gabor,
while reading this thread, I think that there is misunderstanding.
-noaseg flag of recon-all indeed disables using aseg.presurf,
whereas -autorecon2-noaseg does the same thing as -autorecon2-cp
(at least in dev version, looking at the recon-all code).
Antonin Skoch
Hi
Bruce, Gabor,
may I ask, does it ever matter where the midline surface lies? I thought that
this does not affect anything in the analysis.
Antonin
hmmm, if you tar, gzip and upload the subject I'll take a look.
Bruce
On Tue, 26
Sep 2017, Gabor Perlaki wrote:
> I've already corrected a
.$suffix)
The second you overcome by copying the directory
$FREESURFER_HOME/subjects/fsaverage and all its contents of to your
$SUBJECTS_DIR.
Then rerun recon-all on your subject.
Antonin Skoch
Hello all,
I'm having trouble with recon-all on a Linux server, I'm running into the
follo
Dear Antoine,
look here:
http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Antonin
Is it possible to quit the freesurfer mailing list ?
Best regards,
Antoine
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Dear Shadia,
please check, that you really edited your recon.all, as I suggested in my
previous mail. Your recon-all file is located here:
/home/s1163658/freesurferv60/bin/recon-all
According to your recon-all.log, there is still an ln -s command invoked (which
should be replaced by cp command)
so displayed
incorrectly
Antonin Skoch
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The information in this e-mail is intended only for the person to whom it is
addressed. If you be
just a sulcus. I recommend
to assess them using all 3 slice orientations. I correct them by editing wm.mgz
(filling in voxels by value 255).
Regards,
Antonin Skoch
Dear Experts,
This brain looks a little bit strange to us, and I was wondering if someone
might be able to chime in about whether
Dear Matyas,
this (not brain-specific) R package will be maybe more suitable for your
purpose:
http://onlinelibrary.wiley.com/doi/10./2041-210X.12035/full
https://cran.r-project.org/web/packages/geomorph/index.html
I generally would recommend to rather look for packages used in community of
Dear Pradeep,
this issue has appeared several times already here. See following thread:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52560.html
Antonin Skoch
Hello All, My $SUBJECTS_DIR is located on an external disk that was mounted and
recon-all exited with errors at ln -s
o not
know how the resolution of subjects constituting RB_all_2016-05-10.vc700.gca
was, so maybe doing labeling on our 0.7mm3 subjects could lead to even more
accurate results, than option b)? Could you please comment on?
Regards,
Antonin
External Email - Use Caution
Dhivya,
this syntax works for me with version 6. With version 5.3.0 I am getting the
same error mesage. I do not know how the correct syntax is with version 5.3.0.
Antonin Skoch
Yep , I am using "o" .I am running it on Ubuntu 16
External Email - Use Caution
Hi Naomi,
does the symbolic link
/panfs/pan.fsl.byu.edu/scr/usr/74/intj5/analyses/ACAP-BRAVOS/freesurfer/fsaverage
exist in your filesystem?
Antonin Skoch
Hello FreeSurfer Developers,
I'm attempting to run FreeSurfer but I ge
, is here a possibility to estimate it/correct for it?
Regards,
Antonin Skoch
Hi Hugo, they are assumed to be stationary. I've never tried to figure out how
much of a problem this is.doug
On 7/25/12 6:03 PM, Hugo Baggio wrote:
Dear all,I have been performing cortical thickness analyses a
Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of Antonin Skoch
Reply-To: Freesurfer support list
Date: Friday, 17 August 2018 at 18:16
To: "freesurfer@nmr.mgh.harvard.edu"
External Email - Use Caution
Dear Emily,
similar errors I usually try to correct by editing wm.mgz (fill the spots by
intensity 255). But it does not work always (mainly when the hypointensities
are of large extent, it often does not help either).
Antonin
Hi Emily
it's going
sensitivity to clusters with smaller extent but comprising
larger p-values before thresholding.
Antonin Skoch
did you do this?
First, install a new version of mri_glmfit-sim from
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/mri_glmfit-sim
(copy it to $FREESURFER_HOME/bin and
89.
It is in all my processed subjects. Could you please comment on?
Thank you in advance,
Antonin Skoch
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From: on behalf of Antonin Skoch
Reply-To: Antonin Skoch , Freesurfer support list
Date: Tuesday, 2 July 2019 at 21:43
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Doubts in hippocampal subfields labeling
External Email - Use Caution
De
External Email - Use Caution
Hello, Vittal,
do you have image processing toolbox of MATLAB installed? The function fspecial
is part of this toolbox.
Antonin
Hello FS experts,I am trying to run the gyrification index and not able to move
in the right
direction.
When execute th
External Email - Use Caution
Hi Jan,
mri_vol2surf is not the correct command to achieve this.
Use mri_mc or mri_tesselate.
See also
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61335.html
Antonin Skoch
Dear Freesurfer experts,
I would like to run
External Email - Use Caution
Dear Mark,
I would suggest to use PALM instead:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide
PALM supports surface-based data. Each vertex has different area, which has to
be accounted when the cluster size is computed.
Antonin Skoch
check that?
Regards,
Antonin Skoch
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(loaded by
sub-option :label=label_file ) isn't it?
Is it possible to control opacity of surface labels?
Antonin
Od: Ruopeng Wang
Komu: Antonin Skoch , Freesurfer support list
Odesláno: 30.12.2019 19:50
Předmět: Re: [Freesurfer] Freeview - command-line label sub-
External Email - Use Caution
Hi, Tim,
the subject ID can be also contained in the commandline history which is stored
in .mgz files. This can be viewed using
mri_info file.mgz --cmds
I am not aware of any direct command which can strip out this info, but you
surely could conver
images, it leaves images distorted.
For preprocessing of DWI data, I would recommend the "dwipreproc" wrapper
script for FSL tools topup and eddy. This is part of mrtrix3 tool:
https://mrtrix.readthedocs.io/en/latest/reference/scripts/dwipreproc.html
Antonin Skoch
I guess the
even using affine registration would not suffice to precisely
compensate for the distortion.
Antonin
Od: "Yendiki, Anastasia"
Komu: "freesurfer@nmr.mgh.harvard.edu" ,
Antonin Skoch
Odesláno: 7.2.2020 23:44
Předmět: Re: [Freesurfer] DWI EPI correction
External Email - Use Caution
Dear experts,
I began to test beta v7 version of FreeSurfer.
I noticed that some entries in recon-all-status.log seem missing (i.e. white
and pial surface placement - there is entry Cortical Parc while following entry
is Refine Pial Surfs).
Runn
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