External Email - Use Caution I see, thanks. Is there a way in Freesurfer to obtain a visual representation of these results- like in other modalities of group analysis? (eg. surface based)
Many thanks On Tue, 1 Jun 2021 at 17:44, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > 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> <dgr...@mgh.harvard.edu> > *Sent:* 27 May 2021 21:05 > *To:* Aldinhas De Freitas Ferreira, Francisca > <francisca.ferreira...@ucl.ac.uk> <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://secure-web.cisco.com/1YaP5SIsbMLj2enWvcX21X-RXhwYyhkdDK7FxymYtcVWyqhn22STwREvsWceySmxPkzMRE14BruQA3md1iGQUlDQgIXhXmbLrFocUrYBd_1XTbirtq8KEoWa6T-d8bakBhrONca9OqV2t9kmrghoN0cEF5ooJf0hjS-2PsZiQUKAfdQHDi8vmU4OKXCaodt_Lz2wCON8QHfS1PAzzx_zMsUteVUiSwRcDMX2kmkCbCd39Bbi8cAs0r1sadB-0eWoJcwdfV5Fi6eCWmRYNru2hmw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . 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