Thanks for the explanation, Bruce!
Best Regards,
Yi
On 13 Nov 2017, at 5:48 PM, Bruce Fischl wrote:
Hi Yi
yes, brainmask.mgz is the skull stripped image.
And no, n3 is pretty gentle so I would think letting our normal intensity
normalization run would be fine (and better than not doing it)
Hi Yi
yes, brainmask.mgz is the skull stripped image.
And no, n3 is pretty gentle so I would think letting our normal intensity
normalization run would be fine (and better than not doing it)
cheers
Bruce
On Mon, 13 Nov 2017, Yi Li
wrote:
Hi Bruce,
Thanks for the help! Is the skull-stri
Dear experts,
I try to run trac-all -bedp -c dmrirc.tutorial, but error shows like this,
then stop:
INFO: SUBJECTS_DIR is /HD4/DTI
INFO: Diffusion root is HD4/DTI
Actual FREESURFER_HOME /HD2/freesurfer
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this ste
The command looks correct, though I would recommend passing a mask to it
(use the mask.mgh in the glmfit folder). What are the thresholds it
comes up with?
On 11/13/2017 04:41 PM, Hossein Rejali wrote:
>
> Hi,
>
>
> Sorry I am very new to this field, forgive me for ignorance. I am
> trying to
you can use anything that you can register the the FS anatomical
On 11/13/2017 04:34 PM, lanbo Wang wrote:
> Can I use data processed by other tool like FSL, or I can only use DTI
> image after Freesurfer processing?
>
> On Fri, Nov 10, 2017 at 3:07 PM, Douglas Greve
> mailto:gr...@nmr.mgh.harv
Hi Bruce,
Thanks for the help! Is the skull-stripped image in Brainmask.mgz?
Another question: since my raw image has gone through B1 correction and N3
normalization, will you suggest I omit the nu and normalize step in -autorecon1?
Best Regards,
Yi
-Original Message-
From: freesurfer
Hi Hengda
yes, I think you can either use mri_vol2surf or mris_sample_parc to get
your segmentation onto the surface
cheers
Bruce
On Mon, 13 Nov 2017, Hengda He wrote:
> Hi Freesurfer Developers,
>
> I have a manually edited segmentation of the brain cortical regions, and I
> want to map it t
Hi,
Sorry I am very new to this field, forgive me for ignorance. I am trying to do
multiple comparison correction on my data set that I ran through mri_glmfit. I
am currently using mri_fdr as a means for multiple comparison correction. The
problem I am having now is that after running mri_fdr,
Sorry, I forgot the time.dat file. Here it goes.
Thank you,
CP
On Mon, Nov 13, 2017 at 9:28 PM, Conchy PF wrote:
> Dear Douglas,
>
> I did not save the full output from the beginning when I processed this
> subject. I can send you what I get when I run the
>
> mri_glmfit command. If you need t
Can I use data processed by other tool like FSL, or I can only use DTI
image after Freesurfer processing?
On Fri, Nov 10, 2017 at 3:07 PM, Douglas Greve
wrote:
> Yes
>
> On 11/10/17 2:45 PM, lanbo Wang wrote:
>
> Thank you very much, it's work.
> I have another question, this is for structural i
Dear Douglas,
I did not save the full output from the beginning when I processed this
subject. I can send you what I get when I run the
mri_glmfit command. If you need this output, I can run another subject from
the beginning. Please, find attached the original pet data, .nii.gz,
time.dat, and .d
Hi
yes, i can run some subjects and suddenly i get an error.
Actually today i got another kind of error (attach)
And all this only for Hip subfields.
I run fs 6 under neurodebian 8.00 (64b) through virtual box on an i7, 32gb
ram machine and windows 10.
I have an identical machine with same verifica
Can you send the full terminal output? ie, evverything that is printed
to the screen until the program exists? Also, can you send the nii.gz,
.dat, and time.dat file?
On 11/13/2017 03:16 PM, Conchy PF wrote:
> Dear Douglas,
>
> I checked km.ref.tac.dat and these are the values (I also copied th
Dear Douglas,
I checked km.ref.tac.dat and these are the values (I also copied the values
from km.hb.tac.dat):
hbref
26.73126411 -4.761529326
-51.51094818 9.139505029
-44.41317749 -30.22258914
220.9154358 14.15057564
-148.9746399 -43.47668242
616.010437 693.7505493
3824.4064
Hi Freesurfer Developers,
I have a manually edited segmentation of the brain cortical regions, and I
want to map it to cortical parcellation labels on both white matter surface
and pial surface. So I am wondering if there is any way in FreeSurfer that
can map the segmentation volume to cortical la
Hi John,
So you've been able to run some subjects successfully through the subfield
stream? Can you provide some more information like freesurfer
version/buildstamp (run the command ‘bugr') as well as your operating system
and version?
thanks,
Andrew
On Nov 13, 2017, at 7:36 AM, John Papatria
Hi David, please post to the list ... answers below
On 11/13/2017 01:48 PM, David Beeler wrote:
> Hi Doug, really helpful thanks!
> So if I want all the motion corrected functional data across runs to be
> aligned with a downsampled version of my anatomical, is it better to run
> preproc-sess w
Hi Rosalia,
What version of perl are you using? Based on this thread from last year -
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-May/045407.html -
it seems like this is a known issue with new versions of perl and freesurfer
v5.3. Unfortunately, your only two options are to inst
FYI
-- Forwarded message --
Date: Mon, 13 Nov 2017 10:59:30 +
From: Stamatios Sotiropoulos
Reply-To: FSL - FMRIB's Software Library
To: f...@jiscmail.ac.uk
Subject: [FSL] Tenure-Track Research Fellowships in Precision Imaging -
University of Nottingham
Dear All
A number
can you send pics of the two patterns? Also, please remember to post to
the list!
doug
On 11/10/2017 06:16 PM, Fabrizio Pizzagalli wrote:
> Hi Douglas,
>
> I am not obtaining the same pattern testing for Group A > Group B
> (c=[1 -1]) and Group A < Group B (c=[-1 1]).
> That's why I am a bit
Start with funcroi-config. Run it with -help to get documentation
including several examples. Let me know if you still have questions
On 11/11/2017 11:56 AM, Ashley Cole wrote:
> Dear Doug/Bruce,
> I appreciate any insights on this.
> Thank you,
> Ashely
>
>
Please check the reference TAC. Also, please send the full terminal output
On 11/11/2017 06:07 AM, Conchy PF wrote:
> Dear Douglas,
>
> I had the same problem as Jonathan described in his post "PET
> processing seg fault with mri_glmfit --mrtm1"
> (https://mail.nmr.mgh.harvard.edu/pipermail//fr
Is this happening on all subjects or just this one? If just this one,
have you looked at the images to make sure that there is nothing really
wrong?
On 11/12/2017 12:56 PM, Rosalia Dacosta Aguayo wrote:
> My apologizes,
>
> I missed forgot to include the following information:
>
> 1. FreeSurfe
Hi Mel, what resolution are your scans?
doug
On 11/13/2017 09:59 AM, Bruce Fischl wrote:
> Hi Mel
>
> most of the time is usally in mri_ca_register, which does get a big
> benefit from GPU acceleration. mris_inflate should only take a couple
> of min, so I wouldn't worry about it.
>
> Not many
Hi Yi
autorecon1 should do the skull stripping, so there is no need for the
separate mri_mask call. The threshold of '5' is so to preserve edits in
which voxels are turned 'off' (they are set to 1 I believe, but we reserve
2-4 as additional 'off' values).
The masking will not transform the v
Dear FS experts,
I would like to strip skulls from unregistered images which have gone through
GradWarp, B1-correction, N3 normalization and phantom-based scaling. I run the
following two commands in freeSurfer:
recon-all -autorecon1 -subjid
mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz
My q
Hi Mel
most of the time is usally in mri_ca_register, which does get a big benefit
from GPU acceleration. mris_inflate should only take a couple of min, so I
wouldn't worry about it.
Not many recons take 42 hours any more though! That probably means you had
a lot of largish defects. Are you
Dear FreeSurfer users,
I'm using FS 6.0. I registered MRI scans to the CVS-Avg35 template
(mri_cvs_register) and viewed output. While the nonlinear warp of the scan to
the template looked completely fine, the warping of the automatic segmentation
(aseg) did not look as "clean".
Attached is a
Hi,
I was following the instructions here https://surfer.nmr.mgh.
harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview after being told
that the images linked earlier in this email thread were unable to add
white matter (by adding control points) because of a topological defect. I
opened the f
dear Eugenio,
i get the massage randomly after processing 10-15 patients' mri.
And this is only for the subfields.
I run them under the same platform.
John
On Mon, Nov 13, 2017 at 10:45 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:
> Dear John,
>
> This looks like a library error.
Dear list, especially Bruce and Jon,
We are starting to acquire images on the local 7T Philips scanner and would
like to run them through FS. We did some pilot runs following what's
described on http://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon and
in http://www.sciencedirect.com/scie
Dear John,
This looks like a library error. You’re saying that you only get it with some
subjects? Are you running them all on the same platform?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
ht
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