aling
Cheers
Bruce
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *yunus soleymani
*Sent:* Friday, May 3, 2024 3:31 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] surface and cortical thickness normalization
*External Email - Use Caution *
Hello,
I hop
Hi Yunus
I think typically you would normalize by eTIV^(2/3), which would result in a
dimensionless scaling
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of yunus soleymani
Sent: Friday, May 3, 2024 3:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer
External Email - Use Caution
Hello,
I hope you are doing well. Yesterday, I had some questions regarding
normalization in Freesurfer. Thanks to Dr. Douglas N. Greve, I received answers
for all of them. However, I still have one more question.
When I normalize brain surfaces t
behalf of Jiaen Liu
*Sent:* Thursday, April 11, 2024 3:58:18 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] surface-based filtering
External Email - Use Caution
I thought N controls the number of smoothing iterations and the
smoothing in each iteration is defined by fwhm
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Jiaen Liu
Sent: Thursday, April 11, 2024 3:58:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] surface-based filtering
External Email - Use Caution
I thought N controls the number of
...@nmr.mgh.harvard.edu
on behalf of Jiaen Liu
Sent: Thursday, April 11, 2024 3:58:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] surface-based filtering
External Email - Use Caution
I thought N controls the number of smoothing iterations and the smoothing in
each iteration is
certain sigma, where sigma is defined by voxel unit?
Thanks!
Best
Jiaen
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 15:50
To: Freesurfer support list
Subject: Re: [Freesurfer] surface-based filtering
Hi Jiaen
I'm not sure wha
freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 4:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] surface-based filtering
External Email - Use Caution
Hi Bruce
Thanks for your response. In the help, I found the following options. Is
: smooth the target to fwhmtrg
--nsmooth-in N : smooth the input
--nsmooth-out N : smooth the output
Best
Jiaen
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 14:24
To: Freesurfer support list
Subject: Re: [Freesurfer] surface
Yes, we support surface-based smoothing. Check out the help for mri_surf2surf
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 2:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surface-based filtering
External Email - Use Caution
I'm wondering if freesurfer provides functions to filter the surface data
within certain neighborhood exclusively on the surface. It's essentially
similar to regular smoothing in 3D space. But the filtering kernel only runs on
the surface.
I can thin
, 2024 10:50 AM
To: Freesurfer support list
Subject: [Freesurfer] Surface vertex tkr-ras to native T1 RAS without volume
files
External Email - Use Caution
Dear FreeSurfer devs,
I'm writing a program in JavaScript that converts FreeSurfer surface (mesh)
files to other formats,
External Email - Use Caution
Dear FreeSurfer devs,
I'm writing a program in JavaScript that converts FreeSurfer surface (mesh)
files to other formats, which require the vertices to sit in scanner RAS
coordinates.
Right now I'm relying on the FreeSurfer *brain.finalsu
By default, mri_glmfit will "prune" voxels. Ie, if it finds any subject
that is zero at a given voxel, then that voxel is set to zero in the
output and in the mask. I suggest you load up your data
(lh.cbf.fsaverage.proj0.5sm00.nii.gz) as an overlay in freeview and
scroll through the subjects lo
the
actual surface geodesic, but might be good enough?
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Jason Tourville
*Sent:* Wednesday, August 23, 2023 12:27 PM
*To:* Freesurfer support list
*Subject:* [Freesurfer] surface label generation from vertex
might be good enough?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jason Tourville
Sent: Wednesday, August 23, 2023 12:27 PM
To: Freesurfer support list
Subject: [Freesurfer] surface label generation from vertex?
External Email - Use Caution
Hi Freesurfers,
I
External Email - Use Caution
Hi Freesurfers,
I would like to generate a label that extends some distance from a chosen
vertex on the surface. Is this possible in the freeview gui? Otherwise?
Many thanks for you feedback.
Best,
Jason
___
You can use the per-vertex regressor (--pvr) in mri_glmfit. There is
currently no way to correct this for multiple comparisons though.
On 7/13/2022 10:53 AM, Silva Rudberg, Jason wrote:
External Email - Use Caution
Hello Freesurfers,
I am trying to conduct a vertex-wise comparison of
External Email - Use Caution
Hello Freesurfers,
I am trying to conduct a vertex-wise comparison of diffusion MRI and PET data.
I know how to do group vertex-wise comparisons for one imaging outcome (ie.
vertex-wise comparison of a diffusion MRI outcome between two groups). Is th
I don't know much about the infant stream, but you can try running
mris_preproc. See here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0
On 6/7/2022 11:09 AM, Steger Celine wrote:
External Email - Use Caution
Dear FS experts,
We are currently exploring the In
External Email - Use Caution
Dear FS experts,
We are currently exploring the Infant Freesurfer pipeline for surface based
analysis in our cohort. The generated surfaces seem reasonable, but now we are
wondering, how to proceed. To our understanding, by looking at the recon-all
What do you mean by the "total wm measurement"? Total wm volume? If you
are worried about different head sizes, then yes
On 6/1/2022 7:14 AM, Rafael Navarro wrote:
External Email - Use Caution
Hello Dr. Greve,
I am normalizing the cortical SurfArea features from both
?h.aparc.s
External Email - Use Caution
Hello Dr. Greve,
I am normalizing the cortical SurfArea features from both ?h.aparc.stats
with the total white matter surface, calculated as the sum of the total of
the two hemispheres. I checked my results and after applying a t-test I saw
the differ
What surface feature are you exvaluating? If thickness, then don't do
normalization by eTIV or surface area or anything else
On 5/23/2022 11:20 AM, Rafael Navarro wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I am building a brain age model from the stats extracted
External Email - Use Caution
Hello FreeSurfer Developers,
I am building a brain age model from the stats extracted with FreeSurfer. I
tested my model normalizing volumes by eTIV, which I think is the
recommended, and surfaces by WM total surface. For surfaces, I haven't
found any
External Email - Use Caution
Hello FreeSurfer Developers,
Hello, I would like to ask if there are other correction methods besides
multiple comparison correction when surface based group analysis.___
Freesurfer mailing list
Freesurfer@n
That will work; it may be clearer to use mris_fwhm, eg,
mris_fwhm --smooth-only --s sub-0006 --hemi lh --fwhm 5 --cortex --i
input --o output
On 11/26/2021 6:48 AM, Mason Wells wrote:
External Email - Use Caution
Hi Experts,
This question may have been addressed elsewhereon the lis
External Email - Use Caution
Hi Experts,
This question may have been addressed elsewhere on the list, but I can’t find a
response.
I want to smooth BOLD data on the surface. First, I pre-processed the data in
FEAT with no smoothing applied. Then I registered the filtered_func d
So you want to map the labels in fsaverage into MNI152 volumes pace,
right? After mris_divide_parcellation, you should have a parcellation in
fsaverage space. Use mri_surf2surf (or mris_apply_reg) to map that into
the MNI152 that you ran recon-all on. Look in the recon-all.log file for
the comm
External Email - Use Caution
Hi all,
I am having a bit of a hard time figuring out the best option to convert
surface labels to mni volume masks.
For my ROI FS analysis, I divided the fsaverage S1 and M1 labels into 5
sub-labels using mris_divide_parcellation. I then used mri_l
External Email - Use Caution
Dear Greve,
Thank you very much for your reply,
yes indeed i found the problem which was connected to the deletion of 1 slice
of the functional data in order to run the FSL "topup" b02b0.cnf flag.
I solved it by changing this step, using the b02b0
This means that the source or target of the registration is not the same
as what is in the registration file. Did the subject folder change? You
can always delete the registration and rerun, and it will register to
the new target
On 4/9/2021 10:58 AM, Manenti, Giorgio wrote:
> External
External Email - Use Caution
Dear Experts,
I’m encountering a problem when running the preproc-sess on my functional data.
When using the flag -surface subject hemi i am getting ":ERROR: source volume
is neither source nor target of the registration”.
The source is a template.
Sorry for the delay. I actually don't have any programmatic way to force
this change. You can move the surface around in freeview. Under
Tools->RepositionSurface. Change "Intensity" to "Coordinate", then
Shift+Left click near the surface to select the point on the surface you
want to move (ie,
External Email - Use Caution
Hi again, Doug,
I am just checking to make sure that the thread didn't get lost in the pile
of requests, and whether or not you have had a chance to look at the
surfaces I sent.
Thanks
Jake Jensen
On Tue, Oct 6, 2020 at 10:08 AM Jake Jensen
wrote:
External Email - Use Caution
Hi Doug,
just following up to see if you had any suggestions for resolving the
problem of the ?h.wm surfaces not pulling back even after running it
through the pipeline. If you are in need of more screenshots or details,
let me know.
Thanks,
Jacob Je
Can you send pictures of the ?h.orig.nofix surface in addition to the
white and pial?
On 9/29/2020 12:24 PM, Jake Jensen wrote:
External Email - Use Caution
Douglas,
I have attempted to edit the wm.mgz and subsequently run -autorecon2.
However the ?h.white surface remains extended.
It looks like the orig extends too far, so try editing the wm.mgz
On 9/25/2020 11:51 AM, Jake Jensen wrote:
External Email - Use Caution
Attached are a few snapshots of the ?.orig surfaces (pink), pial
(red), and wm (yellow)
On Fri, Sep 25, 2020 at 7:46 AM Douglas N. Greve
mailto:d
External Email - Use Caution
Attached are a few snapshots of the ?.orig surfaces (pink), pial (red), and
wm (yellow)
On Fri, Sep 25, 2020 at 7:46 AM Douglas N. Greve
wrote:
> Can you show it with the ?h.orig surfaces? Those should closely follow the
> boundary of the wm.mgz volu
Can you show it with the ?h.orig surfaces? Those should closely follow
the boundary of the wm.mgz volume
On 9/23/2020 2:11 PM, Jake Jensen wrote:
External Email - Use Caution
Hello,
I am attempting to edit a subject, but upon removing voxels where the
WM and pial surfaces should not
fer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7Cc297cd2860e04ad070c108d7e3113184%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227535305345026&sdata=1W8M039qgGrS3nd3PIh0fbyLyFx1LiD%2FttKnCBD0q9s%3D&reserved=0
>
> On 4/17/2020 10:43 AM, Mason We
01%7CWellsMT1%40cardiff.ac.uk%7Cd1f3f081039a4d49340808d7e2f660e9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227420124409244&sdata=lKy%2B8H9gAxvdLv8vKuqLp3kZ4FdMPlsRgx7AYmVqmvw%3D&reserved=0
>
> On 4/17/2020 10:43 AM, Mason Wells wrote:
>
81039a4d49340808d7e2f660e9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637227420124409244&sdata=lKy%2B8H9gAxvdLv8vKuqLp3kZ4FdMPlsRgx7AYmVqmvw%3D&reserved=0
>
> On 4/17/2020 10:43 AM, Mason Wells wrote:
> > External Email - Use Caution
>
External Email - Use Caution
You will need to convert it to FreeSurfer surface format (instead of MGH/NIFTI,
which are volume formats), the standard one is the binary surface format.
Assuming your file is 'lh.white.gii':
mris_convert lh.white.gii lh.white
or to us
0asSGOSzWzU4yORkEbtrhEknuvs%3D&reserved=0
>
> On 4/17/2020 10:43 AM, Mason Wells wrote:
> > External Email - Use Caution
> >
> > Great, thanks again Bruce.
> > Doug, can you confirm this is the process for taking a fil
s%3D&reserved=0
On 4/17/2020 10:43 AM, Mason Wells wrote:
> External Email - Use Caution
>
> Great, thanks again Bruce.
> Doug, can you confirm this is the process for taking a filtered_func file
and getting it onto the freesurfer surface re
Wells wrote:
> External Email - Use Caution
>
> Great, thanks again Bruce.
> Doug, can you confirm this is the process for taking a filtered_func file and
> getting it onto the freesurfer surface ready for analysis?
>
> Mason T Wells, MSc
> PhD student
> Sch
External Email - Use Caution
Great, thanks again Bruce.
Doug, can you confirm this is the process for taking a filtered_func file and
getting it onto the freesurfer surface ready for analysis?
Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Car
;
>
> I am trying to use an analysis package that works on surface based data
> (SamSrf). I have ran Feat and have a filtered_func file which is of course
> the motion corrected/unwarped version of my EPI. However, I need some
advice
> on how to get these data onto the Free
otion corrected/unwarped version of my EPI. However, I need some
advice
> on how to get these data onto the Freesurfer surface. I have found this
> page, but I wanted to double check this is the most up-to-date pipeline.
On
> the page it suggests using the same DOF as used
ran Feat and have a filtered_func file which is of course
the motion corrected/unwarped version of my EPI. However, I need some advice
on how to get these data onto the Freesurfer surface. I have found this
page, but I wanted to double check this is the most up-to-date pipeline. On
the page it
Hi Marina
can you include command line and full screen output (in text!) so we can
understand what you mean by "it doesn't work". Also, note that
.mgh/.nii.gz are volume formats, not surface ones, so you can't convert a
surface to them. You will need to use our surface format
cheers
Bruce
On
these data onto the Freesurfer surface. I have found this
page<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer>, but I wanted to double
check this is the most up-to-date pipeline. On the page it suggests using the
same DOF as used in Feat, I use BBR so this seems a little redundant. Has
External Email - Use Caution
Hi experts,
How can I convert a surface in .gii format to a surface in .mgh or nii.gz
format?
I tried with mris_convert but it doesn't work.
Best regards,
Marina
___
Freesurfer mailing list
Freesurfer@nmr.
version of my EPI. However, I need some advice on how
to get these data onto the Freesurfer surface. I have found this
page<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer>, but I wanted to double
check this is the most up-to-date pipeline. On the page it suggests using the
same DOF a
at 12:45
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Surface meshes of hippocampal subfields
External Email - Use Caution
Dear Freesurfer experts.
Is it possible to retrieve the mesh representations of the hippocampal
subfields using the latest 7.0 develop
External Email - Use Caution
Dear Freesurfer experts.
Is it possible to retrieve the mesh representations of the hippocampal
subfields using the latest 7.0 development version of segmentHA_T1.sh?
I noticed that the meshes are saved as .txt files in the tmp
directiory (following h
what was your vol2surf command?
why are you masking it to the cortex? This is unnecessary when using
mri_vol2surf
On 2/17/2020 1:13 PM, Marina Fernández wrote:
External Email - Use Caution
Hi experts,
I would like to know how to work correctly on the surface with PET
images to whic
eel.io>
> Sent: Thursday, January 2, 2020 2:06 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Surface file format differences
>
> External Email - Use Caution
>
> Hello,
>
> When working with the nightly development version of FreeSurfer recon-
2020 2:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Surface file format differences
External Email - Use Caution
Hello,
When working with the nightly development version of FreeSurfer recon-all
(freesurfer-linux-centos6_x86_64-dev.tar.gz 23-Dec-2019 06:01)
The su
External Email - Use Caution
Hello,
When working with the nightly development version of FreeSurfer recon-all
(freesurfer-linux-centos6_x86_64-dev.tar.gz 23-Dec-2019 06:01)
The surface file format differed by one character (\n) from previous
versions. What makes me suspicious of t
We are not supporting QDEC anymore. QDEC is running mri_glmfit, which
you can run yourself from the command line. If you seek help, send the
fsgd file and the Xg.dat design matrix
On 11/11/19 7:07 AM, Ferraro, Pilar wrote:
>
> External Email - Use Caution
>
> Hi!
>
> I've previously run
External Email - Use Caution
Hi!
I've previously run a comparison between patients and HC using qdec, but now
I'd like to correct the analysis for disease duration.
I've therefore generated a second qdec.table.dat file inserting the disease
duration column with the following str
External Email - Use Caution
Hi Dr. Fischl
Got it. Thank you very much.
Regards
Raunak Swarnkar
Visiting Student Researcher - Summer 2019
Dept. of Mathematics & Statisitcs, uOttawa
MSc Cognitive Science Student, IIT Gandhinagar
On Mon, Jun 10, 2019 at 3:31 PM Bruce Fischl
wrot
Hi Raunak
you can either load the surface into matlab using read_surf.m or convert
to asci via:
mris_convert lh.white lh.white.asc
cheers
Bruce
On Mon, 10 Jun 2019, Raunak Swarnkar
wrote:
External Email - Use Caution
Dear Dr. Fischl
Thank you for your reply. I was going
External Email - Use Caution
Dear Dr. Fischl
Thank you for your reply. I was going through the same reference earlier.
However, as per my understanding, this page talks about converting a single
point on cortical surface to another space. What I want to achieve is to
extract all t
Hi Raunak
this page should have the info you need:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
cheers
Bruce
On Thu, 6 Jun
2019, Raunak Swarnkar
wrote:
External Email - Use Caution
Hi
I am using freesurfer to extract just the cortical surface mesh. Next, I
External Email - Use Caution
Hi
I am using freesurfer to extract just the cortical surface mesh. Next, I
want to map each vertex on the surface mesh to its corresponding voxel in
the volumetric atlas. Any help how to go forward with it?
Regards
Raunak Swarnkar
Visiting Student Re
Hi Banu
can you send us an image to show us what you mean?
cheers
Bruce
On Tue, 5 Mar 2019, Banu
Femir wrote:
External Email - Use Caution
Hi,
I've a problem about surface placement. For my PhD thesis, I've been analyzing
T1 images of 103 AD,
MCI and SCI subjects. I'm usin
External Email - Use Caution
Hi,
I've a problem about surface placement. For my PhD thesis, I've been
analyzing T1 images of 103 AD, MCI and SCI subjects. I'm using FS 6.0
stable version on Linux.
Some of my data, especially AD data have a surface problem. White matter
includes
oun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, February 15, 2019 1:56:50 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer]
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Friday, February 15, 2019 1:56:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation file ???
you have to create your
rfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, February 14, 2019 3:37:28 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] surface cortical lesions mask --> annota
?
Thank you,
Vale
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Thursday, February 14, 2019 3:37:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface cortical lesions mask --> annotation f
ey
> are in .mgh format
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Greve, Douglas
> N.,Ph.D.
> *Sent:* Thursday, February 14, 2019 3:28:44 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface cortical lesions mask
annotation file for the lesion masks? They are in
.mgh format
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Thursday, February 14, 2019 3:28:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface
not sure what you mean, can you elaborate?
On 2/14/19 2:05 PM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I need to extract annotation files from my cortical lesion masks
> projected to the surface.
>
> Do you know whether this is possible?
>
> Thank you,
>
> Valeria
>
>
> ___
Dear Freesurfers,
I need to extract annotation files from my cortical lesion masks projected to
the surface.
Do you know whether this is possible?
Thank you,
Valeria
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harv
lse I could try?
> >>
> >> Using the SPM GUI, the registration was fine, so I
> thought that
> >> spmregister-sess would have been an improvement, but it
> wasn't.
> >> Is there anyway I can import the registration
Hi Emma
can you run mri_info on the .mgh and .nii.gz volumes and send us the
output? Is the sig.mgh a surface overlay? If so, you can't visualize it
directly, you have to overlay it on a surface (in either .mgh or .nii.gz
foramt)
cheers
Bruce
On Fri, 25 Jan 2019, Bunting, Emma wrote:
Use
mri_concat avg-lh-thickness.15.mgh --std --o avg-lh-thickness.15.std.mgh
You can compute mean with --mean instead of --std
On 1/9/19 9:19 AM, Schranzer René wrote:
>
> External Email - Use Caution
>
> Hello everyone,
>
> I have some problems with the computation of the SD of thickness
External Email - Use Caution
Hello everyone,
I have some problems with the computation of the SD of thickness maps (mgh
file) of 10 subjects.
First I computed the average thickness map (to fsaverage) with the command:
mris_preproc --fsgd qdec/subject_list.fsgd --target fsaverage
External Email - Use Caution
Dear experts,
I have three groups:
- pre treatment (baseline)
- post treatment (follow-up after 6 month of the baseline visit)
- healthy controls.
The three groups have PET data. I ran surface based paired t test between pre
and post treatment. The a
If you have not sampled the PET data onto the surface, you will need to
run mri_coreg to create a registration to the anatomical. Then use can
use mris_preproc with the --iv option (listing each subject with a
different --iv). Run mris_preproc with --help to get examples
On 12/06/2018 12:31 PM,
External Email - Use Caution
Hi Dr Greve,
> I tried to follow this web page
> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> This tutorial seems to be for cortical thickness data. After sampling each
> individual's surface onto the average surface, how can I modify t
?
-- Original --
From: "Bruce Fischl";
Date: Mon, Dec 3, 2018 11:49 PM
To: "Freesurfer support list";
Subject: Re: [Freesurfer] Surface displacement
Hi yujunjie
you need to give us more information than this.
cheers
Bruce
On Mon, 3 Dec 201
Hi yujunjie
you need to give us more information than this.
cheers
Bruce
On Mon, 3 Dec 2018,
1013364183 wrote:
External Email - Use Caution
Dear FS,
We want to calculate the displacement of different surfaces, what should we
do?
yours yujunjie
___
External Email - Use Caution
Dear FS,
We want to calculate the displacement of different surfaces, what should we do?
yours yujunjie___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/lis
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Hi Dr Greve,
I tried to follow this web page
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
This tutorial seems to be for cortical thickness data. After sampling each
individual's surface onto the average surface, how can I modify this comma
Try following this tutorial. It is for fmri, but you can probably apply
it to PET
surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview
Also see you PET module:
surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeview
On 11/20/2018 06:34 PM, john Anderson wrot
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Dear Freesurfer experts,
I would like to run surface based paired t test of PET data on surface. For
every subject I have visit pre treatment and post treatment. I tried to follow
the instructions here https://surfer.nmr.mgh.harvard.edu/fswiki/Paired
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I got today's build, and this issue is gone. The rest of recon-all still
hasn't finished running on my test data but I'll holler if I run into
any other problems. Thanks much!
fsbuild wrote:
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Hello Baxter,
The
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Hello Baxter,
The daily/nightly builds happen at around midnight, so any changes made
today won't get built until midnight. There should be a
new build tomorrow unless something fails the build.
Baxter P. RogersNovembe
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Ah - looking deeper, I think not. I'm not building it locally - I
downloaded today's available compiled version (commit 8abd50c judging by
the build stamp) and it looks like the relevant fix was later, in commit
2720b25. Is there a way to tell what c
did it include the update to mri_tessellate?
On 11/13/18 6:33 PM, Baxter P. Rogers wrote:
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>
> I am still getting the same error with today's build of
> freesurfer-linux-centos7_x86_64-dev.tar.gz
> SHA256 9ea8be61f2f4132770f52459a3e1c746f633727123f9f354953e93
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I am still getting the same error with today's build of
freesurfer-linux-centos7_x86_64-dev.tar.gz
SHA256 9ea8be61f2f4132770f52459a3e1c746f633727123f9f354953e93466dee165c
build-stamp.txt freesurfer-linux-centos7_x86_64-dev-20181113-8abd50c
Thanks,
Bax
I just fixed it
On 11/12/2018 09:35 PM, Bruce Fischl wrote:
> Hi Baxter
>
> we are seeing this locally as well. Probably a bug introduced into
> the last day or two. We will post a fix soon
>
> cheers
> Bruce
>
>
> On Mon, 12 Nov 2018, Baxter P. Rogers wrote:
>
>> External Email - Use Caut
Hi Baxter
we are seeing this locally as well. Probably a bug introduced into
the last day or two. We will post a fix soon
cheers
Bruce
On Mon, 12 Nov 2018, Baxter P. Rogers wrote:
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>
> Hi all - I'm having a problem with recon-all in the current dev version
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Hi all - I'm having a problem with recon-all in the current dev version
of Freesurfer. It is failing somewhere in the surface creation steps. I
get an error during mris_extract_main_component:
ERROR: MRISalloc: nvertices=-1879047998 < 0
No such file
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Got it. Thank you very much for your patient reply.
Best wishes
On Tue, 23 Oct 2018 at 18:59, Bruce Fischl
wrote:
> can you clarify what you mean? We produce two cortical parcellations by
> default (one from Christophe Destrieux and one from Rahul D
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