Hi Richard,
I have attached the log file as you had requested.
Thanks,
On Tue, Feb 28, 2017 at 3:36 AM, R Edgar wrote:
> On 28 February 2017 at 01:10, Francis Tyson Thomas
> wrote:
>
> >
>
> > See utils/test/mriBui
Hi Z K,
I went ahead and tried your suggestion of running *make install *and these
are errors I have,
mv ../../distribution/average/?h.EC_average \
/home/tyson/tyson/fs_install/subjects
chmod -R 775 /home/tyson/tyson/fs_install/subjects/?h.EC_average
rm -Rf /home/tyson/tyson/fs_in
Dear all,
I am carefully starting up with the basics for analysis of 3T mri images.
After having done the recon all I am about to begin the review and editting
process where needed. However, I am now a bit overwhelmed. Is there any
logical or recommended order to proceed with the several potential
Dear all,
I have several different overlays on the same brain surface. When I want to
run freeview in command line and take screenshots automatically, I need to
restart freeview and load the surface for each screenshot. Is it possible
to keep the program on and only change overlays and take screen
On 1 March 2017 at 03:28, Francis Tyson Thomas
wrote:
> I have attached the log file as you had requested.
This is the error:
gzip: testdata.tar.gz: No such file or directory
tar: This does not look like a tar archive
tar: Exiting with failure status due to previous errors
testdata: No such file
Hi All,
I have applied the hippocampal subfield segmentation algorithm to each of my
time points that have been longitudinally processed. I am now trying to
register these back into base space using:
mri_convert -T BASE/mri/transforms/TP_to_base.lta -rl BASE/mri/norm.mgz -rt
nearest --out_ty
Dear Amanda
The longitudinally processed time points are already in base space. Those
transforms you used map base to the original, cross sectionally processed
volumes.
Regarding individual subfields: you can use mri_extract_label to extract
individual labels. You can also obtain probabilistic s
Hi Eugenio,
Thanks for your quick response. It would be great to get the probabilistic
segmentations for each subfield, it's fine if we have to run the segmentation
again. I have only just realised that you now have a longitudinal subfield
segmentation pipeline - is this what I'll need to use?
Hi Peng,
You can write all your freeview commands in a text file and call “freeview -cmd
cmd.txt”. In cmd.txt, just write commands like this line by line:
freeview volume_files -f surface_files … (all the initial file loadings)
freeview (other commands such as -cam) -ss screenshot1.jpg
freeview
Thanks Antonin. For 3) what does " min #of neighbors which must be on to
retain a point/specify fill_holes threshold" mean exactly? Also, I noticed
a difference in FS v5.3 and FS v6.0 ReconAllTable for creating white matter
surface. For v5.3, ?h.white is created as one of the outputs for
mris_make_
Hi Freesurfer Community,
I was trying to run the recon-all for one of the subjects. I got following
error message:
"ERROR: mritotal failed, see transforms/talairach.log".
The image seems to have some missing hippocampal area. I wonder If we can
still run the recon-all?
I checked previous archive
Hello Francis,
Yes, Richard is correct. When doing a local installation you will need the
freesurfer data files which do not come with a default clone of the repo.
Please see section 1.1 of the build page:
$>
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
To get th
Hi Kristine
no, it doesn't. Randy Buckner did a small study on this and found no
detectable effect
cheers
Bruce
On Tue, 28 Feb 2017, Lee Subin Kristine wrote:
> Dear Freesurfer team,
> This may sound like a bit of a small question, but I could not find any
> exact answer elsewhere.
>
> Does th
Hi Redwan,
You'll need to register your volume to an FS-analyzed data set (probably
using bbregister). Then apply mri_vol2surf (run with --help to get examples)
doug
On 2/28/17 5:17 PM, Redwan Maatoug wrote:
Hi all !
I would like to convert my files : volumetrics nifti files to surfaces
f
See if this page will answer your questions
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
On 3/1/17 12:39 AM, Daniel Wen wrote:
Dear Freesurfer experts,
I am new to using freesurfer and was wondering if anyone could explain
to me the difference in output generated by BrainSegVo
I edited the wm.mgz according to the guide, but it didn't change
anything when I ran the reconstruction.
What is the brush value supposed to be when editing? 255?
On Tue, 2017-02-28 at 08:33 -0500,
freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> Send Freesurfer mailing list submissions to
>
Hi,
I am using a volume to create a surface overlay. I am currently overlaying onto
the ?h.inflated volumes created when recon-all is executed. These volumes are
overinflated for what I want. Is there a way I can create a less inflated,
inflated-volume? I was looking at mris_inflate, and was t
sorry, and what is the gordon parcellation?
On 02/28/2017 04:27 PM, Julie Hall wrote:
> 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 f
Not sure about #3, but the final white surface is created by the second
call to mris_make_surfaces. That binary is called twice, the first time
it creates the preaparc file
On 03/01/2017 09:41 AM, miracle ozzoude wrote:
> Thanks Antonin. For 3) what does " min #of neighbors which must be on
>
See this web page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview
On 03/01/2017 09:48 AM, Hari Guragain wrote:
> Hi Freesurfer Community,
>
> I was trying to run the recon-all for one of the subjects. I got
> following error message:
> "ERROR: mritotal failed, see transf
what is your mris_inflate command line?
On 03/01/2017 11:20 AM, Crawford, Anna wrote:
>
> Hi,
>
>
> I am using a volume to create a surface overlay. I am currently
> overlaying onto the ?h.inflated volumes created when recon-all is
> executed. These volumes are overinflated for what I want. Is
I did:
mris_inflate -n 5 wmparc.mgz inflateTest.mgz
I wasn't sure oh what my input file should be. It resulted in the following
message:
No such file or directory
freadFloat: fread failed
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Dougl
yea, you have to run it on a surface, usually the white, eg,
mris_inflate -n 5 -no-save-sulc lh.white lh.inflated.anna
On 03/01/2017 11:45 AM, Crawford, Anna wrote:
> I did:
>
> mris_inflate -n 5 wmparc.mgz inflateTest.mgz
>
> I wasn't sure oh what my input file should be. It resulted in the fo
Got it! Thank you,
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Wednesday, March 1, 2017 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Inflated Volume
yea, you have to run it on a surface,
Hi Antonin, I've verified the problem and am working on a solution.
doug
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 fr
And this is in version 6? What platform are you using?
On 03/01/2017 12:07 PM, Gustav Mårtensson wrote:
>
> Hi,
>
> Yes, running mri_convert
> ADNI_032_S_0187_MRMPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm
>
> dummy.mgh still produces the error
>
> ERROR: GetDICOMInfo(): dc
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 surface labels
Couple of questions:
1)
I edited wm.mgz following the instructions in the wiki guide, but it did
not change anything after reconstruction. I am still using 5.3 right
now, so maybe the guide is wrong for me. What is the brush value
supposed to be? I used 255 but it did not extend the white matter
Hi Douglas.
Thanks for the reply. Forgive me for not responding quickly.
It turns out what we really want is the interim files that are saved during
recon-all if you add the -qcache option. Is there any way to generate those
files after running recon-all without having to run recon-all again
Hi Manuel
have you looked at the aseg? The ventricles are supposed to be filled
automatically using it. What FS version are you using? Usually we don't
want any surface inside the ventricles (which you have a bit of in your
image)
cheers
Bruce
On Wed, 1 Mar 2017, Manuel Delgado wrote:
> Hel
Hi Anna
yes, if you reduce the number of iterations it will inflate less. For
example, from the surf dir:
mris_inflate -n 1 ./lh.smoothwm ./lh.smoothwm.n1
will generate a slightly inflated surface
cheers
Bruce
On Wed, 1 Mar
2017, Crawford, Anna wrote:
>
> Hi,
>
>
> I am using a volume t
Hi Eli
hmm, maybe you should just upload the subject and email us the voxel
coords you are talking about?
Also, in general it is hard for us to help you unless you include more
information. What exact command did you run? What was the screen output?
What was in the recon-all.log?
cheers
Br
HI,
I had reported this issue a while ago and have been trying to track it down
because it seems to be popping up in strange places on our El Capitan and
Sierra machines.
So I initially encountered the error
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenc
Was the subject folder that fails ever uploaded? If not please upload and let
me know when it's ready and I'll take a look. If it was already uploaded try
reuploading as that area get cleared up occasionally.
> On Mar 1, 2017, at 5:17 PM, Mira Michelle Raman wrote:
>
> HI,
>
> I had reporte
Thanks doug. I know the -T flag in mri_fill means min #of neighbors which must
be on to retain a point/specify fill_holes threshold. What does it simply do if
I use it in mri_fill?
Best,
Paul
Sent from my BlackBerry 10 smartphone.
Original Message
From: Douglas N Greve
Sent: Wednesday, M
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/freesurfer@nmr.mgh.harvard.edu/msg32542.html
.thresh labels are thresholded to pick the most likely vertices that give a
l
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 looks like this:
0 Unknown 0 0
Is it possible to run Freesurfer 6.0 recon-all -all on a subject previously
processed with 5.3 and have 6 utilise the wm, ctrl pt and pial edits
(brainmask.finalsurfs.manedit.mgz) made in the 5.3 output? Would it be ok to
run -autorecon2-wm -autorecon3 after renaming aseg.mgz to aseg.presurf.mgz
38 matches
Mail list logo
