Hi all,
I’m trying to compute cortical thickness using mris_thickness (stable 5), but
getting slightly different results from the recon-all 5.1.0-amd64-2.13
(mri_make_surfaces, stable 5).
Hinted from an old thread:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05994.html, I
s
Hi Michael,
I took a look at your data and it seems that you paired a T2 image with
a T1 image when you submitted to recon all. Recon-all will try to
average these together, and since they have such different contrasts,
you will end up with a poor template for surfaces later on.
Try running rec
I have been following the directions on this site to "deploy" (compile) my
MATLAB script so as to be able to run it on launchpad without worrying
about MATLAB licenses.
https://nmr.mgh.harvard.edu/martinos/itgroup/deploytool.html
They say that the deployed script cannot do path manipulations such
Hi all,Would be great is someone can tell me how to exclude user-defined labels from the analysis.As far as I understand after creating all labels, mris_label2annot with a custom colortable should be used.-Is this correct or is there a more efficient way to exclude labels form analysis?-How can the
Hello everyone,
We have 8 spots remaining in our upcoming FreeSurfer course happening on
October 27-29. We will accept late registrations up to the course date;
however, since the payment deadline has passed, payment is due immediately
upon registration.
Details on the course and a link to the
Hi all,
I have been struggling with my .fsgd file. Its header is the following (a total
of 119 subjects):
GroupDescriptorFile1
TitlePatients_vs_Controls
MeasurementNamethickness
ClassPxMale
ClassPxFemale
ClassConMale
ClassConFemale
ClassPxMPRAGE
ClassPxSPGR
Cla
Hi,
In the wiki page on the gyrification index it says that to sample the
results to ico, use
recon-all -s my_subject_id -qcache -measure pial_lgi
If I prefer not to use qudec, can I instead use mris_preproc to do the
registration to atlas and concatenate the files and then use mri_surf2sruf
to
you should be able to use mris_preproc
On 10/9/14 1:08 PM, Lars M. Rimol wrote:
Hi,
In the wiki page on the gyrification index it says that to sample the
results to ico, use
recon-all -s my_subject_id -qcache -measure pial_lgi
If I prefer not to use qudec, can I instead use mris_preproc to d
Each subject can only have one class. So, if you have males and females
who are conotrols and ADs, then you would have 4 classes, and each
subject could only belong to one class
On 10/9/14 11:55 AM, Retzepi, Kallirroi wrote:
Hi all,
I have been struggling with my .fsgd file. Its header is th
What analysis?
On 10/9/14 11:35 AM, Adam, Ruth wrote:
Hi all,
Would be great is someone can tell me how to exclude
user-defined labels from the analysis.
As far as I understand after creating all labels, mris_label2annot
with a custom colortable should be used.
-Is this correct or is there
Hi all,
Sorry for the follow up but hope someone can clarify following doubts.
Thanks,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sneha Pandya
[snp2...@med.cornell.edu]
Sent: Tuesday, October 07, 2014
e: 7
> Date: Thu, 9 Oct 2014 00:12:04 -0400 (EDT)
> From: "Reza Rajimehr"
> Subject: Re: [Freesurfer] rawfunc2surf-sess with a limited set of
> surface files
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <42178.18.93.15.69.1412827924.squir...@mai
Try added something like "-expkey iter05". When you make the analysis
you will have to spec "-stem fmc.iter05"
doug
On 10/09/2014 12:12 AM, Reza Rajimehr wrote:
> Hi Doug,
>
> Removing -i fmc did not help, and I still get the same error.
>
> By looking at the rawfunc2surf-sess script, it looks
Thanks Doug! I got it to work. The outputs are like
fmc.sm2.F99.lh.iter05.nii.gz
Should I still specify stem as fmc.iter05 in mkanalysis-sess?
Reza
Try added something like "-expkey iter05". When you make the analysis
you will have to spec "-stem fmc.iter05"
doug
On 10/09/2014 12:12 AM, Rez
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