External Email - Use Caution
Thanks for the info, Dr. Greve!
So for the files I used for the --y argument were stacked files of this file:
lh.long.thickness-spc.fwhm10.fsaverage.mgh or
rh.long.thickness-spc.fwhm10.fsaverage.mgh.
So would my interpretation of the ocn.dat file be
External Email - Use Caution
Hi FreeSurfer team,
After running longitudinal FS, and running mri_glmfit using files that measured
spc, we found clusters associated with our continuous variable (WMH volume)
after controlling for other covariates. I was wondering though, do the
file should I use? Would it still
be the mri_segstats command, but without the --avgwf option?
Thanks again for your help and time!
Batool
From: Douglas N. Greve
Sent: Monday, August 24, 2020 10:11 AM
To: Rizvi, Batool ; Freesurfer support list
Subject: Re: [Freesurfer] extracting beta
External Email - Use Caution
Dear FreeSurfer experts,
After running the longitudinal pipeline with QDEC, I needed beta-values of the
associations between my main continuous variable and the significant cortical
cluster, as well as of all the nuisance factors/categorical
area? Just
wondering, as we only performed QDEC using thickness so far.
Thanks so much,
Batool
From: Rizvi, Batool
Sent: Tuesday, November 28, 2017 3:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: QDEC and comparing two conditions
Hi FreeSurfer experts,
We calculated the correlation between
Hi FreeSurfer experts,
We calculated the correlation between thickness two different behavioral
conditions using QDEC. We now want to compare the spatial overlap and
difference in thickness-correlation between the two behavioral conditions. We
would like to do this both visually as well as
Hi,
I'm running tracula using the following command:
(Note: I'm replacing actual paths with made up paths)
trac-all -prep -c /path/to/my/config.sh
And for some reason it stops running while working on the first subject
(creates the folder for the first subject), with this error:
if: Expression
edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Rizvi, Batool"
<br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, Mar
urfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool
[br2...@cumc.columbia.edu]
Sent: Wednesday, March 29, 2017 9:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions
Thank you. That m
that have 49.
Best,
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool
[br2...@cumc.columbia.edu]
Sent: Wednesday, March 29, 2017 8:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA
Hi,
We were wondering if it would be an issue if we used a dataset in which we
included 5 subjects that have a different number of directions (49 directions)
than the rest of the subjects with a standard number (16 directions). Even if
the preprocessing steps work, will it be an issue
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 23 Feb 2017, at 20:11, Rizvi, Batool
<br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote:
Hi,
I was wondering if the hippocampal subfields analysis can still run on a lower
resolution T1 scan than 1mm? One of
Hi,
I was wondering if the hippocampal subfields analysis can still run on a lower
resolution T1 scan than 1mm? One of our datasets has T1 scans with these
dimensions: .93 x .93 x 1.3 .
Would it still run on this dataset, if it's not the standard 1mm to begin with?
Thanks!
Batool
)
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 13 Feb 2017, at 17:04, Rizvi, Batool
<br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote:
Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 13 Feb 2017, at 16:41, Rizvi, Batool
<br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> wrote:
Hi,
I'm having trouble gettin
Hi,
I'm having trouble getting any output from the hippocampal subfield analysis
command. I entered in:
quantifyHippocampalSubfields.sh T1 hippo.txt
/path/to/my/subjects/freesurferfolder
I tried both ways of having the environmental variable subjects directory
defined to the freesurfer folder
consensus is "how many subjects do you have?" -- if it's
less than 50, you may want to just rerun v6 on your subjects as it should
preserve the edits -- but it's recommended you still open them up and double
check.
-Adam
On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool
<
already processed all my data with 5.3, but am interested
in getting hippocampal subfields through 6.0.
Thanks so much!
Batool
From: Rizvi, Batool
Sent: Wednesday, January 25, 2017 12:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: freesurfer 6.0 with some
Hi,
I'm wondering if it's okay to run some of the analyses within one study on
v.5.3 and the other hippocampal analyses on 6.0? Or do you recommend us
starting over for the analyses we've already done in 5.3 for that study?
Thank you!
Batool
___
-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool
[br2...@cumc.columbia.edu]
Sent: Wednesday, December 14, 2016 1:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] incorrect pial surfaces after watershed adjustment
Ohkay thanks, we'll go ahead and run autorecon2 and autorecon 3
Bruce
On
Wed, 14 Dec 2016, Rizvi, Batool wrote:
>
> Hi FreeSurfer experts,
>
>
>
> We have a subject on which we had to do adjust the watershed parameters for,
> since there was some
> brain missing from the brainmask.mgz. The watershed itself worked, but after
> that
?
cheers
Bruce
On Mon, 12 Dec 2016,
Rizvi, Batool wrote:
>
> Hi Bruce,
> We re-ran these subjects using recon-all -all -autorecon2-cp -aurorecon3
> -subjid freesurferfolder.
> We got no output files from that, but I'm wondering if freesurfer didn't run
> only because we incorrectl
01, 2016 5:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
change
sure, good luck
Bruce
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
> Sounds great, thanks again for your help and will try out your
> recommendations.
> Have a
Hi FreeSurfer team,
We have a couple of subjects that have really poor segmentation and skull-strip
as well, that seem beyond fixing with just control points or WM edits. I'm
wondering if this occurred because of earlier in the stream, there was a bad
talairach transform? I went back to see
2016, Rizvi, Batool wrote:
>
> Hi Bruce,
> Thanks so much for the feedback, that is very helpful. We'll try deleting the
> control points then. Is there a quick way to rerun recon-all without having
> it take up to 5-8 hours?
>
> Also, a separate question, when running a
a bit in that entire region (by the ratio of 110/103).
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
> Hi Bruce,
> Thanks for your reply. It is actually brighter on the brainmask.mgz than the
> orig.mgz when I checked. I'm uploading the freesurfer subject here.
>
&g
possible to diagnose from a single slice from a single subject. If
you tar, gzip and upload the subject one of us will take a look
cheers
Bruce
On Thu, 1
Dec 2016, Rizvi, Batool wrote:
>
> Hi FreeSurfer experts,
>
>
>
> After running -autorecon2 and -autorecon3, we're seei
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