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You should have a look at the 'aparcstats2table' command that comes with
FreeSurfer, it does exactly what you want. There is no need to compute this
manually.
https://secure-web.cisco.com/1y8MoV_lySYxRtn11tB5a6H64yS1J9YFCgCSFtxDPRbXFecgkVvEyZqopn8AN3
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Oh sorry, ignore my last mail, I misread your question. aparcstats2table will
compute the values for native space, and if I interpret your email correctly,
you want them in standard space.
Sorry for the confusion,
Tim
> On 10/08/2021 8:28 AM Dongyu
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Dear Freesurfer community,
I am using the freesurfer version through a singularity container
(https://secure-web.cisco.com/1j_Zv2QItcuWtdQRfU3BocTH20Tz0V5FYnvMZKQNUHVHrSJnEYT6SaYNXa25BmI-JbPTJCJ1GCrzzhmfuUc3ZZ6iK4JDuJS0kjv_hdt8Wl2-pAx2OFoyTnLpSWLjFHa
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Yes,I want to compute them in standard space.But I don't know which atlas I
should use?
> -原始邮件-
> 发件人: "Tim Schäfer"
> 发送时间: 2021-10-08 15:27:32 (星期五)
> 收件人: "Freesurfer support list"
> 抄送:
> 主题: Re: [Freesurfer] Confusion about mean CT m
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Hi Rana,
The samseg tool in FreeSurfer will segment some non-brain tissues. If
that's not sufficient for your needs, you can also check out a more
specialized version of samseg distributed with the new/upcoming version of
SimNIBS -- cf.
https://secure-
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Hi Randolph,
When you visualize the segmentation produced by samseg on top of its input
image, does the segmentation look correct? If so, the problem is very
likely not the affine registration code. (If the segmentation looks bad,
please try samseg in
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Yes,I want to compute them in standard space.But I don't know which atlas I
should use? > -原始邮件- > 发件人: "Tim Schäfer" > 发送时间:
2021-10-08 15:27:32 (星期五) > 收件人: "Freesurfer support list"
> 抄送: > 主题: Re: [Freesurfer] Confusion about
mean CT m
what happens if you run it without the mask?
On 9/29/2021 2:33 PM, Pedersen, Walker Scott wrote:
I just wanted to follow up on this - based on the output I sent
previously, they seem to have the same resolution (unless I've missed
something). They do have different orientations. Could this be
Have you seen this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
On 9/30/2021 1:08 AM, Abbie Taing wrote:
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Hi all,
I have a between subjects factor (3 groups) and within subjects factor
(3 stimuli type). I am interested in comparing cortica
Look in the recon-all.log file for the command that creates the
aparc+aseg.mgz. Change the annotation to be the annotation that you want
to use, and change the name of the output file.
On 9/30/2021 10:07 AM, Ahmed Radwan wrote:
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>
> Dear FreeSurfer experts,
The wm.mgz is expected since we added denoising to it; but it does not
matter because wm.mgz is essentially a binary mask of WM. The
brainmask.mgz is created from T1.mgz. The T1.mgz will be affected by
control points, but only if you run it from the beginning. The surfaces
are placed on brain.f
You need to add matlab to your path. If you type
which matlab
it will indicate whether it is in your path or not
On 10/1/2021 3:51 PM, Camila Fernandes da Silva wrote:
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Hey,
I'm totally new into Freesurfer and I need some help with my Matlab.
I tried to do "
If you subtract them, eg,
fscalc vol1.mgz sub vol2.mgz abs gte 0.5 -o diff.mgz
This command will subtract the two, take the absolute values, then
threshold (binarize) the differences.
I'm not sure what you are looking for in terms of aparc+aseg, but you
can do something like
mri_segstats --ctab-
The volume is the volume of cortex only, not the volume of subcortical
structures. We don't have a VBM-style analysis that would be needed for
subcortical GM. You can always do an ROI analysis, asegstats2table and
mri_glmfit with --table option; this will allow you to analyze the
volume of each
Sorry, I'm not sure what you are asking when you ask what you should do.
Do about what?
On 10/4/2021 5:30 AM, Annalisa Lella wrote:
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Dear Mr. Greve,
thanks so much for your reply! I have been running t-tests on cortica
The frequency of the low pass filter (lpf) must be greater than the high
pass filter. Why did you set it to 0?
On 9/30/2021 8:27 PM, Nasiriavanaki, Zahra,M.D. wrote:
Hi Freesurfer experts,
I was wondering how many seeds we can use in fcseedcor command? I have
more than 100 seeds and when I us
On 10/4/2021 7:09 PM, Giuseppe Miranda wrote:
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Hello,
I have been looking through tutorials on the website and referencing
the freesurfer mail archives, but I am a bit unsure if I am following
the correct procedures for my analysis. The main source of co
If I run without the mask, the output sig file looks normal. If I overlay the
surface ROI and the output sig file on the fsaverage, I can see that the
maximum absolute pvalue in my ROI is around -2.2. Output below. Since the mask
is based on a volumetric sphere, it is not contiguous after conve
External Email - Use CautionI have elaborated all my data with recon all version 7.0. I am doubting whether I should elaborate them again with 7.2 or I can simply run the normalisation with 7.2 on the data preprocessed with 7.0, since you told me that the problem with version 7.0 i
Sorry, I don't know what h5 format is.
On 10/5/2021 4:30 AM, I. Kelleher-Unger wrote:
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>
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>
> Hi there,
>
> I have used fmriprep to preprocess my BOLD data. One of the outputs of this
> pipeline is a T1w-to-MNI transfor
It might be that the format is too new for our code. Have you tried
dcm2niix? We are currently incorporating dcm2niix backend into
mri_convert, but we're not there yet.
On 10/6/2021 2:36 PM, Rizzo, Nolan W wrote:
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Hello FreeSurfer developers,
I am attempt
what were your recon-all commands?
On 10/2/2021 4:55 PM, Kevin Miller wrote:
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The mri_diff command did show differences after re-running the wm and
skullstrip commands under different names, but the differences were
not related to the areas that I was trou
It has been replaced by thalamus now
On 10/8/2021 6:56 AM, Cubillo, Ana wrote:
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Dear Freesurfer community,
I am using the freesurfer version through a singularity container
(*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" c
You want to measure cortical thickness in standard space? It is not
something we typically do, but I guess you could apply the taliarach
registration to the surfaces and recompute the thickenss, eg,
mris_apply_reg --lta lh.white ../mri/transforms/talairach.lta lh.white.tal
mris_apply_reg --lta l
What do you mean it is based on a volumentric sphere? How did you
create it?
On 10/8/2021 1:24 PM, Pedersen, Walker Scott wrote:
If I run without the mask, the output sig file looks normal. If I
overlay the surface ROI and the output sig file on the fsaverage, I
can see that the maximum abs
What do you mean by "elaborated"?
On 10/8/2021 1:29 PM, Annalisa Lella wrote:
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I have elaborated all my data with recon all version 7.0. I am
doubting whether I should elaborate them again with 7.2 or I can
simply run
External Email - Use CautionPre-processed with recon allIl 8 ott 2021 19:50, "Douglas N. Greve" ha scritto:
What do you mean by "elaborated"?
On 10/8/2021 1:29 PM, Annalisa Lella
wrote:
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Cauti
I used afni's 3dundump to create a 10mm sphere from MNI coordinates. I then ran
the MNI template through freesurfer, and used the regheader from this to run
mri_vol2surf to put the spherical ROI into fsaverage space. I am able to
overlay the ROI created this way onto the fsaverage in freeview, a
If you have not done manual editing, then just rerun in 7.2 from scratch
On 10/8/2021 1:52 PM, Annalisa Lella wrote:
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Pre-processed with recon all
Il 8 ott 2021 19:50, "Douglas N. Greve" ha
scritto:
What do you
I'm not sure what is going on. Try these two things
1. Binarize the mask (if not already) with mri_binarize --i yourmask.mgz
--min 0.1 --o binmask.mgz
2. Try adding --no-cortex (since you already have a mask, you don't need
to spec cortex)
On 10/8/2021 2:01 PM, Pedersen, Walker Scott wrot
Can you just read it in with python or something and write it out in one of our
supported formats (like .lta)?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Friday, October 8, 2021 1:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject:
External Email - Use CautionThat's what I wanted to avoid: reprocess all the data. Am I forced to? Il 8 ott 2021 19:52, Annalisa Lella ha scritto:External Email - Use CautionPre-processed with recon allIl 8 ott 2021 19:50, "Douglas N. Greve" ha scritto:
What d
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For skullstrip: recon-all -skullstrip -wsthresh 15 -clean-bm -subjid
For wm: recon-all -autorecon2-wm -autorecon3 -subjid
> On Oct 8, 2021, at 12:40 PM, Douglas N. Greve wrote:
>
> what were your recon-all commands?
>
> On 10/2/2021 4:55 PM, Kev
It will be the easiest. If you have not edited them, then it is just
computer time, right?
On 10/8/2021 2:38 PM, Annalisa Lella wrote:
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That's what I wanted to avoid: reprocess all the data. Am I forced to?
Il 8 ott 20
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Hello,
Thank you for your reply. I went back and checked the brain.finalsurfs.mgz and
it is changing the values to 110 and looks much better. The aseg.mgz is also
looking better after the edits as well.
When we typically do successive passes through
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Hi Experts,
If I want to analyze and visualize baseline and follow-up for an individual
subject's change (before-after & after-before). Should I treat it as a
cross-sectional analysis for a group analysis?
Best,
Zeno
_
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Dear FreeSurfer experts:
I want to know cortical thickness in this file
'subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh' is in standard space or in
native space.
Is not the common coordinate system the same as standard space?
And if mean ROI CT
On 10/8/2021 8:51 PM, Dongyue Zhou wrote:
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Dear FreeSurfer experts:
I want to know cortical thickness in this file
'subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh' is in standard
space or in native space.
standard
Is not the common coordinate sy
I don't know what you mean. Can you elaborate?
On 10/8/2021 5:27 PM, Zeng, Qi wrote:
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Hi Experts,
If I want to analyze and visualize baseline and follow-up for an
individual subject's change (before-after & after-before). Should I
treat it as a cross-se
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Dear FreeSurfer experts:
I use the 'qcache' command to get the file
'$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'.
Now,I have known that cortical thickness in this file is in standard space.But
I don't understand why it is an
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Dear FreeSurfer experts:
I use the 'qcache' command to get the file
'$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'.
Now,I have known that cortical thickness in this file is in standard space.But
I don't understand why it is an
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