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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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 dgreve@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 CautionSo 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 dgreve@mgh.harvard.edu *Sent:* 27 May 2021 21:05 *To:* Aldinhas De Freitas Ferreira, Francisca francisca.ferreira.16@ucl.ac.uk 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:
External Email - Use CautionDear 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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1aa2SiyojiXB68BwDW7pBUi7Bb4E8YBIfrdOl8sVnGWmr6B... 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-RXhwYyhkdDK7FxymYtcVWyqhn... . 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.
Not easily. You can do something in matlab, eg,
aseg = MRIread('fsaverage/mri/aseg.mgz'); out = aseg; out.vol = zeros(out.volsize); ind = find(aseg.vol==17); % 17 = left hippo out.vol(ind) = YourValueForLeftHippoFromTheGLMAnalysis; % same thing for other ROIs MRIwrite(out,'sig.aseg.mgz'); Then visualize on the fsaverage volume
On 6/1/2021 6:14 PM, Francisca Ferreira wrote:
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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 <dgreve@mgh.harvard.edu mailto:dgreve@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 <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Sent:* 27 May 2021 21:05 *To:* Aldinhas De Freitas Ferreira, Francisca <francisca.ferreira.16@ucl.ac.uk> <mailto: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: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, FranciscaThe 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://www.massgeneralbrigham.org/complianceline <http://secure-web.cisco.com/1YaP5SIsbMLj2enWvcX21X-RXhwYyhkdDK7FxymYtcVWyqhn22STwREvsWceySmxPkzMRE14BruQA3md1iGQUlDQgIXhXmbLrFocUrYBd_1XTbirtq8KEoWa6T-d8bakBhrONca9OqV2t9kmrghoN0cEF5ooJf0hjS-2PsZiQUKAfdQHDi8vmU4OKXCaodt_Lz2wCON8QHfS1PAzzx_zMsUteVUiSwRcDMX2kmkCbCd39Bbi8cAs0r1sadB-0eWoJcwdfV5Fi6eCWmRYNru2hmw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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). 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