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:

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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 <dgreve@mgh.harvard.edu>
Sent: 27 May 2021 21:05
To: Aldinhas De Freitas Ferreira, Francisca <francisca.ferreira.16@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:

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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

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