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Hi dear freesurfer list.
I want to run recon-all command on 400 NIFTI images using laptop connected
to my universty supercomputer
How can I do that?? Any help
And what about the organization of data structure
I'm new to neuroimaging, as well as Linux
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Dear Anastasia,
Thank you so much for the response. Interestingly, when I try to open the two
reconstructed brains at the same time, they don't overlay. Am I correct to
assume then that we have to run recon-all using version 7.2.0? I'm providing a
s
I have made some edits to this recently. Can you try the new one?
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkheadsurf
guest
collab
On 1/7/2022 11:11 AM, Yong-Jun Lin wrote:
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Hello FreeSurfer Developers,
I was attempting to execute the mkheadsurf s
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
Hi, I don't know what is causing the discrepancy. Try taking the table
input that you are passing to SPSS and pass it to mri_glmfit with the
--table option. Oftentimes the SPSS model ends up being different than
the model using by mri_glmfit. There could also be some issues with
poorly conditio
The direction cosines (DCs) for the row, col, and slice.
The DCs for the row and column are obtained from DICOM (20,37),
which is a string of the form "cx\cy\cz\rx\ry\rz". The slice DC is
obtained from the ASCII header. The x, y, and z components are from
three lines of the form "sSli
I don't know what the schaefer atlas is, but in principle it should work
On 1/10/2022 3:55 PM, Julie Ottoy wrote:
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Hi Doug
Thank you, worked as a charm!
I was wondering if I can apply this code on other atlases, for example
I have the schaefer atlas (in M
I think the issue may be the use of commas (,) instead of decimal points
(.). You an convert it easily with
cat yourfsgd | sed 's/,/\./g' > yournewfsgd
On 1/12/2022 12:10 PM, Laura Willers de Souza wrote:
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Hello FreeSurfer Developers,
I want to perform an
It is probably reasonable to correct for either TIV or total HTh volume.
Each of these tests a different hypothesis, so just know what hypothesis
you are testing.
On 1/12/2022 10:32 PM, Xiaotong Zhang wrote:
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In the statistical analysis of the volume of th
You can use eg, -auto-runseq mgz, this will unpack all scans as
runno.seqname.mgz (eg, 0004.mprage.mgz). You might want to add
-no-exit-on-error so that it does not exit when it finds a run that it
cannot convert.
On 1/14/2022 8:44 PM, Shi, Yuelin wrote:
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You can run mris_preproc to get a stack of the thicknesses (one frame
for each subject), then run
mri_concat stack.mgz --mean --o mean.mgz
Then load the mean with
tksurferfv fsaverage lh inflated -aparc -ov mean.mgz -fminmax .01 3
On 1/15/2022 7:37 PM, Fischl, Bruce wrote:
Hi Rahul
If you hav
When you say movement "correction" here I'm assuming you mean including
regressors. I don't have anything that will compute the 24 regressors
you mention. But if you have something that will, you can create a table
that has a row for each time point and 24 columns, then pass it to
mkanalysis-se
On 1/21/2022 7:49 AM, 刘卫 wrote:
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Hello FreeSurfer Developers,
Hello, I would like to ask if there are other correction methods besides
multiple comparison correction when surface based group analysis.
You can use FDR (mri_fdr)
Can I use the 6.0 versio
what version of FS are you using?
On 1/21/2022 2:21 PM, Goeckner, Bryna wrote:
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Hi,
I am trying to decide how to proceed after manually updating a
talairach since various ways I’ve tried the recon process give me
different results.
Our group used Freesu
Not sure about #1 and #2, and #4 depends on those. For #3, the age
Variable will regress out age. The time diff variable will regress out
the effect of duration.
On 1/21/2022 8:19 PM, Zeng, Qi wrote:
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Hi,
I got a couple of questions regarding group analys
I think that should work.
One other issue is that the wm.seg.mgz might need to be uchar (a relic
of when computers did not have so much memory). If it does not work with
falk's command, you can try
mri_convert -odt uchar --no_scale 1 wm.seg.mgz wm.seg.mgz
On 1/24/2022 2:47 AM, falk.luesebr...@m
I'm not sure what is happening or why the tal reg is apparently failing.
My guess is that it is something non-standard about the image. The first
thing to try is to run it at 1mm (without the -hires). At some point,
you may have to send us the volume (or at least some pictures in axial,
sag, an
you should ask the supercomputer administrators
On 1/26/2022 12:24 PM, REEM ABU BAKR BAHATHIQ wrote:
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Hi dear freesurfer list.
I want to run recon-all command on 400 NIFTI images using laptop
connected to my universty supercomputer
How can I do that?? Any
what happens if you convert it to an mgz file and then use mri_info to
look at the orientation string?
On 1/11/2022 11:52 AM, Xiaojiang Yang wrote:
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Dear Freesurfer Developers,
I have scrutinized the Freesurfer source code from github, found that this
migh
Sorry, the developer of this program has moved on in her career so we
have no one to support it anymore. We maybe looking at it again in the
next year or so.
On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote:
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>
> Dear all
>
> as some other posted before me, so
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