There are not results to visualize, there is just a table. There should
be a sig table in the output folder
On 5/28/2021 9:37 AM, Aldinhas De Freitas Ferreira, Francisca wrote:
External Email - Use Caution
So so sorry to bother you again - hopefully the last time...
I have followed your suggestion and that has worked, having used this
command
mri_glmfit \--table aseg_stats.txt \--fsgd newCH_deblank3.fsgd dods
\--C groupdiff.mtx \--glmdir aseg.glmdir
I am now trying to visualise the results according to FSwiki, used
this command
freeview -f
/usr/local/freesurfer/subjects:annot=aparc.annot:annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/F.mgh:overlay_threshold=20,50
-viewport 3d
I get the following error
ERROR: reading /usr/local/freesurfer/subjects
Read 0 bytes, expected 1
Read 0 bytes, expected 1
/freesurfer/subjects
MRISread failed
I wonder is this means there is something wrong with the GLM I created
or if it is something wrong with my Freeview?
Thanks a lot in advance!
Kind regards,
Francisca
------------------------------------------------------------------------
*From:* Douglas N. Greve <dgr...@mgh.harvard.edu>
*Sent:* 27 May 2021 21:05
*To:* Aldinhas De Freitas Ferreira, Francisca
<francisca.ferreira...@ucl.ac.uk>
*Subject:* Re: Freesurfer- subcortical group analysis
Hi Francisca, if you run asegstats2table on your group to create a
group table (subjects on the rows, structures on the columns, each
element being the structure volume for that subject), then you can use
mri_glmfit with the --table option (instead of --y). You may want to
correct for intracranial volume by adding --etiv to the
asegstats2table command.
doug
On 5/27/2021 7:13 AM, Aldinhas De Freitas Ferreira, Francisca wrote:
External Email - Use Caution
Dear Dr Greve,
My name is Francisca Ferreira, I am a neurosurgeon/neuroimaging PhD
student at the FIL in UCL. I have recently contacted Eugenio
Iglesias, who kindly pointed me in your direction. Sorry to bother
you, I have been working with Freesurfer and I was hoping you would
kindly give me your opinion?
I am looking to compare responders vs non responders to deep brain
stimulation of a subcortical structure called ventral tegmental area.
I ran recon-all, and thought Freesurfer could be useful for this task
as it now has a brainstem segmenting module that I’ve installed.
I thought I could use brainstem or subcortical volumes/surfaces to do
the glm group analysis? (in my case regressing out age and gender).
It seems that all the options i found on mri_glm only allow
surface-based analysis? (the flags available being - - cortex or -
-non-cortex) is there any way around this?
I am sorry for any lack of background knowledge- which stems from the
fact that I am primarily a clinician...
I’d be most grateful for any suggestions!
Kind regards,
Francisca
The information in this e-mail is intended only for the person to whom
it is addressed. If you believe this e-mail was sent to you in error
and the e-mail contains patient information, please contact the Mass
General Brigham Compliance HelpLine at
http://www.massgeneralbrigham.org/complianceline . If the e-mail was
sent to you in error but does not contain patient information, please
contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not
wish to continue communication over unencrypted e-mail, please notify
the sender of this message immediately. Continuing to send or respond
to e-mail after receiving this message means you understand and accept
this risk and wish to continue to communicate over unencrypted e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If
the e-mail was sent to you in error but does not contain patient information,
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
