Dear all,
I wanted to ask you a question about longitudinal TRACULA analysis. I'm
analyzing a group of patients with different time points. In my configuration
file, I used "affine registration from the individual T1 to the MNI T1 template
with FLIRT and a correlation ratio cost" as the inter-su
No, there is not an easy way to break it up that way. If you know some
programming, you could merge all 3 into one seg, then compute the PCA of
the coordinates, then divide it up along the largest direction
On 9/9/2024 1:54 AM, Necati Emre Şahin wrote:
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De
External Email - Use Caution
Dear FreeSurfer Developers,
I hope this message finds you well.
I am currently working with FreeSurfer 7.4.1 and I have encountered a situation
that I would like your guidance on. Specifically, I have noticed that
FreeSurfer outputs the lateral ve
...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez, Juan
E.
Sent: Tuesday, August 27, 2024 3:13 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Question on hippocampus segmentation algorithm
Dear Alice:
1. Can you please send another capture without the mask, or with the option
“show
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Savoia, Alice (Stud. FPN)
Date: Tuesday, August 27, 2024 at 7:00 AM
To: Freesurfer support list
Subject: [Freesurfer] Question on hippocampus segmentation algorithm
External Email - Use Caution
Hi everyone!
I have segmented the hippocampus subfields using the segmentation tool provided
by the latest version of FreeSurfer. I am now looking at the pictures and I
have a few questions:
*
In some cases, the hp tail takes a bit of the thalamus,
ake a look?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Siegel, Nys Tjade
Sent: Monday, August 5, 2024 9:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Question/potential bug regarding mri_convert and .gca
files
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Dear
External Email - Use Caution
Dear Freesurfer community,
I'm trying to extract labels from a .gca atlas volume using the following
command:
mri_convert atlas.gca -nth 1 labels.mgz (from
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GcaFormat)
I've found a .gca file in
I'm not sure what you mean. Usually, one would edit the proper volumes
in freeview using the protocol described (eg, setting edited voxels to
certain values). One can implement automatic edits as long as one keeps
to the protocol.
On 7/30/2024 5:09 PM, Edwards, Vincent wrote:
Externa
External Email - Use Caution
Hello Freesurfer team!
We are editing brain scans using T1/T2 mutual information to improve the
original image. Are the recon-all flags the same with as they would be when
editing using only the T1 images (i.e., recon-all -cp, -pial, -wm), or are
the
please send your command line, terminal output, and stats file
On 7/23/2024 3:07 PM, Selena Gangaram wrote:
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Hi,
I hope you are doing well, I subscribed to your mailing list to ask my
question!
I was wondering if you knew the reason as to why my extracti
External Email - Use Caution
Hi,
I hope you are doing well, I subscribed to your mailing list to ask my question!
I was wondering if you knew the reason as to why my extraction code in
FreeSurfer listed regions such as "Whole_hippocampal_body" amongst other brain
regions twice
,
Lilla,Ph.D.
Subject: Re: [Freesurfer] question about infantfreesurfer
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What I mean is that it's a beta version, so I just wanted to make sure that I
can use these results in a publication.
Knut Jørgen Bj
External Email - Use Caution
What I mean is that it's a beta version, so I just wanted to make sure that I
can use these results in a publication.
Knut Jørgen Bjuland
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://ma
Hi Knut,
Can you clarify what you mean by your question?
Lilla
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Knut J Bjuland
Sent: Friday, April 5, 2024 2:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] question about infantfreesurfer
ited by available developer
> time.
>
>
>
> BW,
>
> Henry
>
>
>
> *From: *Georgios Argyropoulos
> *Date: *Friday, 12 April 2024 at 11:04
> *To: *Tregidgo, Henry
> *Cc: *freesurfer@nmr.mgh.harvard.edu
> *Subject: *Re: [Freesurfer] Question on using
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Question on using thalseg_1.1.h5
many thanks, Henry, that's super helpful. Btw, I came across the
segmentThalamicNuclei_DTI.sh here
(https://secure-web.cisc
ions. A clue to this is the deprecation warning
> mentioning numpy version 1.25 as the version in fspython is 1.24.3
>
>
>
> *From: *Georgios Argyropoulos
> *Date: *Thursday, 11 April 2024 at 17:24
> *To: *freesurfer@nmr.mgh.harvard.edu ,
> Tregidgo, Henry
> *Subject
: Georgios Argyropoulos
Date: Thursday, 11 April 2024 at 17:24
To: freesurfer@nmr.mgh.harvard.edu , Tregidgo,
Henry
Subject: Re: [Freesurfer] Question on using thalseg_1.1.h5
⚠ Caution: External sender
Many thanks and apologies, Henry - I figured it out... I stupidly replaced your
improved
External Email - Use Caution
Many thanks and apologies, Henry - I figured it out... I stupidly replaced
your improved segmentation script in both the scripts and the bin directory
instead of only replacing the former.
many thanks for your time, much appreciated
g
you been able to run the segmentation using the packaged model?
Best wishes,
Henry
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Georgios Argyropoulos
Date: Thursday, 4 April 2024 at 00:53
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Question on using thalseg_1.1.h5
⚠
External Email - Use Caution
Dear freesufer experts,
Does anyone know whether infantFreesurfer is ready to use for publication
purposes? Thank you! Knut Jørgen Bjuland, PhD Telemark Hospital
___
Freesurfer mailing list
Freesurfer@nmr.mg
the above fails, then you should contact whoever setup the machine, your IT
department, etc. and ask them to provide write permission there.
- R,
Begin forwarded message:From: XinRan Wu <wxr1173199...@gmail.com>
Subject: [Freesurfer] Question about mris_compute_lgi error:
/s
External Email - Use Caution
Dear Colleagues,
Hope you're well.
I have been trying to use the thalseg_1.1.h5 patch (MRI Segment Thalamic
Nuclei CNN model v1.1 update). I use the following command:
mri_segment_thalamic_nuclei_dti_cnn --t1 mri/norm.dwispace.mgz --aseg
mri/aseg.dwi
External Email - Use Caution
I am a researcher currently working with the Freesurfer 7.1.1 version for a
research project. I have encountered an issue while trying to compute the
local gyrification index (LGI).
We have pre-existing Freesurfer analysis results, and we want to use t
Hello there,
When we were trying the TRACULA tutorial, we noticed a discrepancy between the
downloaded script and the wiki page. The echo spacing is set as 0.000689998 in
the script, but it is exemplified in ms on the wiki page. For the epifactor, it
is set as 139000.96811584961115829321 in the
External Email - Use Caution
Hi Reza,
The lesion class in samseg is a bit special, as the internal lesion
probabilities are thresholded (using the value passed on via the
--threshold flag, or a default value 0.3 if you didn't use that flag) to
obtain the voxels labeled as 99 in th
External Email - Use Caution
Hi freesurfer
I did an experiment about lesions about the output of samseg. And the
results are as follows:
The volume of lesions in label 99 in seg.mgz result is 745 mm^3.
The samseg output for lesions in samseg.stats is 633 mm^3.
Is it ok? Why are
External Email - Use Caution
Thanks
The volume of lesions in label 99 in seg.mgz result is 745 mm^3.
The samseg output for lesions in samseg.stats is 633 mm^3.
Is it ok?
On Thu, Nov 16, 2023, 5:57 PM Douglas N. Greve
wrote:
> Internally, samseg uses partial volume to compute a
Internally, samseg uses partial volume to compute a more accurate
volume. They should still be very close though.
On 11/16/2023 6:46 AM, reza razmara wrote:
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Hi freesurfer team
I use samseg for lesion segmentation. In the result of .stats i see
the lesion
External Email - Use Caution
Hi freesurfer team
I use samseg for lesion segmentation. In the result of .stats i see the
lesions volume. But when i extract lesions seprately as a new file we know
that it uses the label 99 for extraction. But when i calculate the volume
of this extr
Q8FV7PEIuiLy1z3HVp3gbjCsii3j4j03rTzmmPs5FUP-VmkbKWIa7_dLCtbBDJidWYD2UEyV7ab5r6eKb0byoeD5Qd53y4Iok2NVwnUXajXd4ZCe1R8wQt8Ndoe2_mSWLSLu8ae6eDQHoXaJeC_iT1Z1F4-j4b4v9uBN0Fdvvw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer>
>>>
>>> It suggests using mri_coreg.
>>>
>>&
gh.harvard.edu%2Ffswiki%2FPetSurferIt
suggests using
mri_coreg.-PaulFrom: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Mahdi Babaei <mahdibabai...@gmail.com>Sent: Sunday,
November 5, 2023 2:25 PMTo: freesur...@nmr.mgh.harvard.eduSubject:
[Fr
4ZCe1R8wQt8Ndoe2_mSWLSLu8ae6eDQHoXaJeC_iT1Z1F4-j4b4v9uBN0Fdvvw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer>
>>
>> It suggests using mri_coreg.
>>
>> -Paul
>>
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu <
>>
nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Question about Freesurfer
External Email - Use Caution
Dear FreeSurfer Team,
I'm currently a PhD student at Stevens Institute of Technology in New Jersey,
USA, where my research focuses on MRI to PET tra
harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mahdi Babaei <
> mahdibabai...@gmail.com>
> Sent: Sunday, November 5, 2023 2:25 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Question about Freesurfer
>
> External Ema
tSurfer
It suggests using mri_coreg.
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Mahdi Babaei
Sent: Sunday, November 5, 2023 2:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Question about Freesurfer
External
External Email - Use Caution
Dear FreeSurfer Team,
I'm currently a PhD student at Stevens Institute of Technology in New
Jersey, USA, where my research focuses on MRI to PET translation. I have a
number of problems. Freeview opens fine but when I load a column in it just
shows a b
I doubt it. Have you tested it and found otherwise?
On 6/14/2023 3:23 PM, ruifen...@gmail.com wrote:
External Email - Use Caution
Hi all,
I am running Freesurfer 7.3.2 on T1 images (LPI orientation) with
176*256*256 FOV, 1mm isotropic resolution.
I saw that the Ants N4 bias correct
External Email - Use Caution
On 8/9/2023 5:03 AM, inbal paran wrote:
External Email - Use Caution
Dear FreeSurfer developers,
Thank you for your response to my previous questions, I have a few
more (I'm inexperienced with both Freesurfer and Linux):
1. Can I visualize
External Email - Use Caution
Dear FreeSurfer developers,
Thank you for your response to my previous questions, I have a few more
(I'm inexperienced with both Freesurfer and Linux):
1. Can I visualize my results after running mri_glmfit by using Freeview,
such that the image shows
External Email - Use Caution
It is worse -- we do not support qdec anymore
On 8/5/2023 6:04 AM, inbal paran wrote:
External Email - Use Caution
Hello FreeSurfer Developers, I have a question regarding group
analysis: When I followed the instructions on how to build my
External Email - Use Caution
Hello FreeSurfer Developers,
I have a question regarding group analysis:
When I followed the instructions on how to build my FSGD file,
it said that:"FSGD files are created automatically by qdec, but qdec
is currently (12/9/08)
limited to two continuou
arvard.edu
*Subject:* [Freesurfer] Question about mri_convert --conform
*External Email - Use Caution *
Hi all,
My input 001.mgz has data type short, but converted to
unsigned byte. The plot shows the intensity of thee two
images. How is the data conve
>>
>>
>> Best,
>>
>>
>>
>> Yujing
>>
>>
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *
>> ruifen...@gmail.com
>> *Sent:* Thursday, May 25, 2023 2
s -nc (nochange) flag to mri_convert to keep the
original data type.
Best,
Yujing
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of
*ruifen...@gmail.com
*Sent:* Thursday, May 25, 2023 2:45 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Que
t; freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *ruifen...@gmail.com
> *Sent:* Thursday, May 25, 2023 2:45 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Question about mri_convert --conform
>
>
>
> *External Email - Use Caution*
External Email - Use Caution
Hi all,
I am running Freesurfer 7.3.2 on T1 images (LPI orientation) with
176*256*256 FOV, 1mm isotropic resolution.
I saw that the Ants N4 bias correction is done after the FOV is expanded to
256*256*256, not on the original image. Shouldn't t
@nmr.mgh.harvard.edu
Subject: [Freesurfer] Question about mri_convert --conform
External Email - Use Caution
Hi all,
My input 001.mgz has data type short, but converted to unsigned byte. The plot
shows the intensity of thee two images. How is the data conversion done? Thanks.
Best,
Ruifeng
External Email - Use Caution
Hi all,
My input 001.mgz has data type short, but converted to unsigned byte. The
plot shows the intensity of thee two images. How is the data conversion
done? Thanks.
Best,
Ruifeng
___
Freesurfer ma
External Email - Use Caution
Dear freesurfer experts,
recently I update freesurfer to freesurfer 7.4.0 under Ubuntu 20.04. when I try
to launch freeview, I get error message as:
freeview
This application failed to start because no Qt platform plugin could be
initialized. Reins
External Email - Use Caution
7.4.0 will show up on the rel7 downloads page and will be announced on the
freesurfer mailing list once it has been released. Until then, anything
you were able to find/download should be deleted as it is incomplete.
- R.
On May 11, 2023, at 08:27,
External Email - Use Caution
Hi,
I wanted to install the new freesurfer version v7.4.0, but when I entered the
downloads page I realized that it's not showing up on the downloads page as of
yet
(https://secure-web.cisco.com/1Ik7kyPTfqcfyovpF4HdOSDjavPlUIQiKi3ICy0S1I64cgfUQ7jmauV
External Email - Use Caution
Hi,
I am trying to use EasyReg to obtain the forward field from registering a
functional slab (partial FOV) to an anatomical (T1-weighted) scan.I know that
EasyReg currently does not support functional slabs. So the deformation with
our slab looked v
rd.edu
*Subject:* Re: [Freesurfer] Question about volumetric atlas ROIs overlap
External Email - Use Caution
I don't understand what you are referring to. Can you elaborate?
On 5/5/2023 7:53 PM, Nadvar, Negin wrote:
External Email - Use Caution
Hello,
I have a general questio
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, May 8, 2023 10:47 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Question about volumetric atlas ROIs overlap
External Email - Use Caution
I don't understand what you are referr
External Email - Use Caution
I don't understand what you are referring to. Can you elaborate?
On 5/5/2023 7:53 PM, Nadvar, Negin wrote:
External Email - Use Caution
Hello,
I have a general question about handing atlas ROIs after applying
recon-all on a T1W image. Coul
External Email - Use Caution
Hello,
I have a general question about handing atlas ROIs after applying recon-all on
a T1W image. Could you please clarify how I can minimize/prevent atlas ROIs
overlap in volumetric subject-specific space when going from surface-based
space to vol
: Thursday, March 16, 2023 at 10:12 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Question on EasyReg forward field
External Email - Use Caution
Hi,
I am trying to shift the statistical maps that I obtained from a second-level
fMRI analysis (meaning across multipl
16, 2023 at 10:05 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Question on easy reg
External Email - Use Caution
Hi,
I have tried to use the EasyReg package to obtain the forward field by
registering a functional slab to the structural (with skull) of a sub
Reply-To: Freesurfer support list
Date: Thursday, March 16, 2023 at 10:03 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Question on EasyReg package syntax
External Email - Use Caution
Hi,
I have tried to use EasyReg.
I have tried to use the following syntax t
External Email - Use Caution
Hi,
I am trying to shift the statistical maps that I obtained from a second-level
fMRI analysis (meaning across multiple sessions for one subject).
My plan is to use EasyReg to align the functional data to the structural data.
Based on the resulting
External Email - Use Caution
Hi,
I have tried to use the EasyReg package to obtain the forward field by
registering a functional slab to the structural (with skull) of a subject.This
doesn't seem to work, do you know what may be the issue?
Many thanks,Codrin
_
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Hi,
I have tried to use EasyReg.
I have tried to use the following syntax to generate the output of EasyReg and
it didn't seem to work:
mri_easyreg --ref structural1.nii.gz --flo structural2.nii.gz --ref_seg
segmentation_reference --flo_seg segmentat
Hi Philipp, by default, those parameters are not used anymore as we are
using ANTS N4 (though this is not obvious). There is no separate
parameter set for for 3T for N4. It is still possible to use the old
MNI N3 code, so we have kept it in there.
On 2/25/2023 2:58 PM, Saemann, Philipp wrote
External Email - Use Caution
Hi FreeSurfer specialists,
we have problems with a strong non-intensity in 3 Tesla data of GE (mainly
temporal poles and occipital area).
We managed to rescue the occipital errors by a pre-Bias-field correction using
SPM, but would of course try
t
External Email - Use Caution
I do not get the cingulate, for example...
On Wed, Dec 21, 2022 at 4:35 PM Rosalia Dacosta Aguayo
wrote:
> Hi Douglas,
>
> I am only getting the main volumes like putamen right and left, amygdala,
> right and left...just gross anatomy.
>
> Rosie
>
External Email - Use Caution
Hi Douglas,
I am only getting the main volumes like putamen right and left, amygdala,
right and left...just gross anatomy.
Rosie
On Wed, Dec 21, 2022 at 4:32 PM Douglas N. Greve
wrote:
> what are you not getting?
>
> On 12/21/2022 10:11 AM, Ros
what are you not getting?
On 12/21/2022 10:11 AM, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Maybe is -qcache ?
*
*
On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo
wrote:
Dear Freesurfer group,
Could you tell me which is the flag I need to use t
External Email - Use Caution
Maybe is -qcache ?
On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo
wrote:
> Dear Freesurfer group,
>
> Could you tell me which is the flag I need to use to get all the brain
> parcellation when I run recon-all? It seems I am getting the tab
External Email - Use Caution
Dear Freesurfer group,
Could you tell me which is the flag I need to use to get all the brain
parcellation when I run recon-all? It seems I am getting the tables with
few volumes and I guess there is something wrong.
Best wishes and Merry Christmas,
it would be helpful to see some images. Also send the log file
On 11/9/2022 6:47 AM, dimitra kokkinou wrote:
External Email - Use Caution
Dear freesurfer experts,
I am analysing some MP2RAGE images on freesurfer and found an error I
am unable to correct.
After the recon-all finishe
FS does not warp any images. No smoothing is ever applied.
On 11/7/2022 3:30 PM, Katrina Simon wrote:
External Email - Use Caution
Hi, I have a dataset i have run with the default settings of
Freesurfer 6.0. A reviewer for a paper recently raised the question
"Were T1 images warped w
External Email - Use Caution
Dear freesurfer experts,
I am analysing some MP2RAGE images on freesurfer and found an error I am unable
to correct.
After the recon-all finished successfully, I looked at the T1 and brainmask
images on freeview and I noticed a skullstripping error
are you looking at a surface or a volume? for volume, there is an
opacity slider in freeview
On 10/28/2022 11:06 PM, Yoshito Saito wrote:
External Email - Use Caution
Hello.
I would like to ask a question about the color look-up table.
I want to change the opacity of color on a brain
On 10/26/2022 10:05 PM, Lyna Mariam El Haffaf wrote:
External Email - Use Caution
Hi!
I hope you are doing well!
I am working on a paper where we used Freesurfer for whole brain
analysis in intergroup comparison (g2v1). The objective of the
analysis is to see if there is an assoc
External Email - Use Caution
Hi, I have a dataset i have run with the default settings of Freesurfer
6.0. A reviewer for a paper recently raised the question "Were T1 images
warped with the grey matter preserved? Were volumetric images for the
amygdala and hippocampus smoothed?"
I
External Email - Use Caution
Hello.
I would like to ask a question about the color look-up table.
I want to change the opacity of color on a brain atlas in Freeview. I
changed the number in a column of opacity in the Color Lookup Table file by
following the instructions on this we
External Email - Use Caution
Hi!
I hope you are doing well!
I am working on a paper where we used Freesurfer for whole brain analysis in
intergroup comparison (g2v1). The objective of the analysis is to see if there
is an association between neuropsychiatric symptoms and brain
This is a known bug. Please see
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
for a patch
On 10/14/2022 1:46 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
I receive an error when I try to run the sclimbic module, do you have
any sugge
External Email - Use Caution
I receive an error when I try to run the sclimbic module, do you have any
suggestions on why this might be happening? : Loaded input image from
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/GP1462~1/mri/nu.mgz
Traceback (most recent call last):
File
first of all, send us the log file
On 9/5/2022 8:53 PM, zhoudong...@mail.dlut.edu.cn wrote:
External Email - Use Caution
Dear FreeSurfer experts:
I updated Freesurfer 7.0.0 on my ubantu system, but there is something
wrong so that I can't finish running recon-all pipieline.
External Email - Use Caution
Dear FreeSurfer experts: I updated Freesurfer 7.0.0 on my ubantu system,
but there is something wrong so that I can't finish running recon-all
pipieline. It stopped at mris_fill in auto-recon2.And I don't know why. It
didn't happen when I use
On 3/24/2022 2:53 AM, Dongyue Zhou wrote:
External Email - Use Caution
Dear FreeSurfer experts:
I want to calculate mean pial surface area in DKatlas in individual
space.And I know the function read_annotation.m in $FREESURFER_HOME/matlab for
loading this atlas.
And if I ca
, not of the surface. Don’t you
want the mean across subjects, not across vertices within a subject?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Dongyue Zhou
Sent: Saturday, March 26, 2022 1:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Question
External Email - Use Caution
Dear FreeSurfer experts:I want to calculate mean pial surface area in
DKatlas in individual space.And I know the function read_annotation.m in
$FREESURFER_HOME/matlab for loading this atlas.And if I can load
sub/surf/?h.area.pial as the area
External Email - Use Caution
Dear FreeSurfer experts:I want to calculate mean pial surface area in
DKatlas in individual space.And I know the function read_annotation.m in
$FREESURFER_HOME/matlab for loading this atlas.And if I can load
sub/surf/?h.area.pial as the area
behalf of Trisanna Sprung-Much
Date: Wednesday, March 2, 2022 at 11:07 AM
To: Freesurfer support list
Subject: [Freesurfer] Question about editing topology errors
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Hi there
I have this issue occurring in several hemispheres (See images attached) where
a
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Hi there
I have this issue occurring in several hemispheres (See images attached) where
a “sulcus” is created because the pial crosses where it shouldn’t, and am
wondering what the best way to edit this is. I don’t think it is a matter of
adding WM
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Right!
Thank you so much!
Best,
Laura.
De: Douglas N. Greve
Enviado: sábado, 19 de fevereiro de 2022 18:37
Para: Laura Willers de Souza
Cc: freesurfer@nmr.mgh.harvard.edu
Assunto: Re: [Freesurfer] Question glm
-
*De:* Douglas N. Greve
*Enviado:* quinta-feira, 17 de fevereiro de 2022 20:25
*Para:* Laura Willers de Souza
*Assunto:* Re: [Freesurfer] Question glm analysis g4v0
No, that was only for interactions between the covariates and the groups
On 2/17/2022 10:05 AM, Laura Willers de Souza
__
De: Douglas N. Greve
Enviado: quinta-feira, 17 de fevereiro de 2022 20:25
Para: Laura Willers de Souza
Assunto: Re: [Freesurfer] Question glm analysis g4v0
No, that was only for interactions between the covariates and the groups
On 2/17/2022 10:05 AM, Laura Willers de Souza wrote:
External
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Hello FreeSurfer Developers,
I am performing a GLM analysis to assess cortical thickness between 4 groups,
without any covariates. I followed exactly what is on the wiki
https://secure-web.cisco.com/1VuhMA49mKmIDKH_rGPy4c67MdbjL6bNv2i_WwNDwvMA5-MXr
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Hello FreeSurfer Developers,
I am performing a GLM analysis to assess cortical thickness between 4 groups,
without any covariates. I followed exactly what is on the wiki
https://secure-web.cisco.com/1OE5gTnSPStX6C1rqwHBKIDpqIcnp_2ymvTKb8n7oDB8IxXRDqg
On 1/8/2022 3:25 AM, zhoudong...@mail.dlut.edu.cn wrote:
Dear FreeSurfer experts:
I am confused how vertex position is determined. Is the vertex's
position on surface is determined?
Each vertex in fsaverage is mapped back to the surfaces of 40 subjects.
The xyz for the vertex is the mean
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Dear experts:
I performed cluster-wise correction for along-tract measures using
mri_glmfit-sim as documented here (
https://secure-web.cisco.com/1YmsMw8LA5K4vjKmpPSbf5iYXXniVrshoE73mbH13u44IuoBXZGKk-S1LT6gy3CSkRwBjaZ6oMN-qgBbeAYvsunDCNhABi1e1g5GIRMOfK
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I don't know the internal details for FreeSurfer, maybe others can help with
those. But in general, the vertices and faces are constructed *together* from
the (pre-processed) image voxels by algorithms like Marching Cubes:
https://secure-web.cisco
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Hi dongyue,
The distance between vertices differs. Roughly speaking, areas with higher
curvature show higher vertex density.
As for your first question, I am not sure what exactly you mean, could you
explain in more detail what you want to know?
T
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Dear FreeSurfer experts:
I am confused how vertex position is determined. Is the vertex's position on
surface is determined? And is the distance between each two vertex the same？
Bests，
dongyue
External Email - Use Caution
External Email - Use Caution
Dear FreeSurfer experts:
I am confused how vertex position is determined. Is the vertex's position on
surface is determined? And is the distance between each two vertex the same？
Bests，
dongyue
External Email - Use Caution
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