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).
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 correct
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
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
ls (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-optio
?
Regards,
Antonin Skoch
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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
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
://www.jeiglesias.com
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
89.
It is in all my processed subjects. Could you please comment on?
Thank you in advance,
Antonin Skoch
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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
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"
, 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
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 get
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
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 Skoch
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 $SUBJECTS_DIR is located on an external disk that was mounted and
recon-all exited with errors at ln -s
Dear Matyas,
this (not brain-specific) R package will be maybe more suitable for your
purpose:
http://onlinelibrary.wiley.com/doi/10./2041-210X.12035/full
https://cran.r-project.org/web/packages/geomorph/index.html
I generally would recommend to rather look for packages used in community
it is just a sulcus. I recommend
to assess them using all 3 slice orientations. I correct them by editing wm.mgz
(filling in voxels by value 255).
Regards,
Antonin Skoch
Dear Experts,
This brain looks a little bit strange to us, and I was wondering if someone
might be able to chime in about whether
so displayed
incorrectly
Antonin Skoch
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you be
Dear Shadia,
please check, that you really edited your recon.all, as I suggested in my
previous mail. Your recon-all file is located here:
/home/s1163658/freesurferv60/bin/recon-all
According to your recon-all.log, there is still an ln -s command invoked (which
should be replaced by cp
Dear Antoine,
look here:
http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Antonin
Is it possible to quit the freesurfer mailing list ?
Best regards,
Antoine
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
.$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
following error
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
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
-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 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
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https
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,
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
___
Freesurfer mailing list
Freesurfer
u/pub/dist/freesurfer/dev/freesurfer-Linux-centos6_x86_64-dev.tar.gz
How is the build of dev version sheduled?
Antonin Skoch
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information
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
___
Freesurfer mailing list
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 <a...@ikem.cz> wrote:
> Dear
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
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
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
-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
be >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 Skoch
D
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
?
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 number
>
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
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
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
interpolation could have such profound effect !
I will try your suggestions and let you know.
Antonin
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
To: Antonin Skoch <a...@ikem.cz>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Sent: 4/21/2017 1:00 AM
Subject: Re:
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.com/freesurfer
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
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 04/13/20
?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
/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 Time
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
that the 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
on?
Regards,
Antonin Skoch
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e
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 <a...@ikem.cz>
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
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
= (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
. Could you please comment
on?
Regards,
Antonin Skoch
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
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
!
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
ptions 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
advise how to diagnose and solve the error?
I am using development version from beginning of february 2017.
Regards,
Antonin Skoch
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Mar 10, 2017 at 1:58 AM, Antonin Skoch <a...@ikem.cz> 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 as Anderson said, the values can a
mmands I am using to run the analysis?
Thanks a lot,
Sahil
On Wed, Mar 8, 2017 at 11:54 PM, Antonin Skoch <a...@ikem.cz> wrote:
> Dear Sahil,
>
> to assure that there is no other issue with your setup, I would recommend to
> obtain cluster-wise p-pvalue
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 <a...@ikem.cz> wrote:
> Dear Sahil,
>
> to assure that there is no other issue with your setup, I would recommend to
> obtain clu
and area maps?
Thanks you so much Antonin for all your help.
Sahil
On Wed, Mar 8, 2017 at 3:05 PM, Antonin Skoch <a...@ikem.cz> 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 an
ot Antonin.
Sahil
On Wed, Mar 8, 2017 at 2:06 PM, Antonin Skoch <a...@ikem.cz> 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?
>
>>>
>>> - Include -logp, so that the p-values are in log-10 scale. Significant
>>> p-values are then those above 1.3 (i.e., -log10(0.05). This will help to
>>> make the figures nicer later.
>>>
>>> All the best,
>>>
>>
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
ect?
On Tue, Mar 7, 2017 at 3:48 PM, Antonin Skoch <a...@ikem.cz> 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 h
)
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 <a...@ikem.cz> wrote:
> Dear Martin,
>
> input -i input file is
>
> lh.MEQ_LGI.10.mgh file in your glmdir directory (for left hemisphere).
)
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 <a...@ikem.cz> wrote:
> Dear Martin,
>
> input -i input file is
>
> lh.MEQ_LGI.10.mgh file in your glmdir directory (for left hemisphere).
xpert in using FreeSurfer, 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, Ant
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
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=FSL=0&1=FSL&9=A=on=No+Match%3BMatch%3BMatches=4=239088
but beware not to forget to include average the vertex area
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 23:28:11 greve
>
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)
-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-archive.com
2017 at 5:41 PM, Antonin Skoch <a...@ikem.cz> 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 fsa
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
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 <a...@ikem.cz> wrote:
> Dear Paul,
>
> I suppose the clue is following messages from your recon-all.log file:
>
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
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
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
, 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
are overlapping and I
would need to correctly assign vertices in the label intersection (see my
previous post
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51919.html ).
Regards,
Antonin
Try adding --no-unknown to the label2annot command line
On 02/28/2017 04:45 PM, Antonin Skoch
you in advance for clarification.
Regards,
Antonin Skoch
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
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
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
___
Freesurfer
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
. 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 implementation
<freesurfer-boun...@nmr.mgh.harvard.edu> namens Antonin Skoch <a...@ikem.cz>
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 a
<freesurfer-boun...@nmr.mgh.harvard.edu> namens Antonin Skoch <a...@ikem.cz>
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 r
/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
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 matrix
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
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
are 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
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
1 - 100 of 170 matches
Mail list logo
