[Freesurfer] mri_glm fit: gd2mtx method dods--C unrecoginzied
External Email - Use Caution Dear Experts, I am new to FS. I'm trying to run mri_glm fit I've created FSGD with 2 classes -responders vs non-responders to a given intervention- and 3 variables to be regressed out-according age, gender, laterality. I've made my FSGD file is made in accordance with documented FS directions. I've created the contrast vector in accordance to Nregressors and it works out to be 1 -1 0 0 0 0 0 0 I add I'm using DODS to do this task. the constructed command I used is this mri_glmfit \--y lh_test.smoothed10FWHM.mgh \--fsgd newCH.fsgd dods\--C groupdiff.mtx \--surf fsaverage lh\--cortex \--glmdir lh.test.glmdir 1) The first problem encountered is INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done I have tried to demean my data adding the flag --demean, which I found in more than one forum, but i think this is an incorrect flag as it didnt work anyway. 2) I have constructed my contrast vector also in accordance with FS directions, in a text editor adding the extension .mtx I'm getting this error ERROR: gd2mtx method dods--C unrecoginzied. Legal values are dods, doss, and none. Help would be much appreciated. KR F. Ferreira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
External Email - Use Caution Dear Experts, I have extracted subcortical vols corrected for intracranial vols using asegstats2table and I ran mri_glmfit using the following command mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C groupdiff.mtx \--glmdir aseg.glmdir this seems to have worked. I am now trying to visualise my results adapting the recommended wiki command freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5 -viewport 3d Freeview crashes and I'm getting the following error Number of vertices in overlay data (64 or 64) does not match with surface (163842). Number of vertices in overlay data (64 or 64) does not match with surface (163842). Is there something wrong with the commands priot to this step? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
External Email - Use Caution Hi Doug, I ran mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C groupdiff.mtx \--glmdir aseg.glmdir this created a folder aseg.glmdir which contains another folder groupdiff, where sig.ghm is, I then tried to visualise results using freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5 -viewport 3d Many thanks in advance! Francisca On Tue, Jun 1, 2021 at 1:40 AM Douglas N. Greve wrote: > How did you create the sig.mgh that you are trying to overlay? > > On 5/28/2021 11:16 AM, Francisca Ferreira wrote: > > External Email - Use Caution > Dear Experts, > > I have extracted subcortical vols corrected for intracranial vols using > asegstats2table and I ran mri_glmfit using the following command > > mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C > groupdiff.mtx \--glmdir aseg.glmdir > > this seems to have worked. > I am now trying to visualise my results adapting the recommended wiki > command > > freeview -f > /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5 > -viewport 3d > > Freeview crashes and I'm getting the following error > > Number of vertices in overlay data (64 or 64) does not match with surface > (163842). > Number of vertices in overlay data (64 or 64) does not match with surface > (163842). > > Is there something wrong with the commands priot to this step? > > > > > > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1dYHFn7zS6B646bWS9lFLOInJlhX5O-D2krlFdkSw8d8E87WUGXoPX-5ZIjvu5BZgJGqV4WcKBC8HZ5ngAJCv5uwvhDEhDjesPMvsPecL4LixYYDUXswY3Mk_4ZVP8VjlzSUERHT6fBiwa2YCF359vMYgXHvhrUMDOkb7f0keLG7BP6EGKV2lh7rk_OgigOKCd8jF0dvfM2btGPhw8_jWl7oNkLp9eHIYq--EonKLebQull7L8D_DuHSTmL-RI6I09hqvXMCPvzhYxdzPCGHdHg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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/1dz6MBaZ4CWlcN057t5KUwTLiDxU7Gt4GlmynrD0X76B3ja_x_8lvda9ONecmoOo9l-H8ED-qe4-YpazYh8RrGkprEjor9AwgaXrL5xKS6cX1580zuuYucQcGCRgIUnmJZZCuE1OJ0vecTWAuWdLmJ71AUd9271Y1x8BiROUHvP9gkqmZwOzPn8zZW-MGIlZAfjFTVb556fGMu8qNrPBVJmVjp-R6s-6akYYuUXn_Dou4pstNV9bM4MmirQXcc8eLgVEzjZieBZ_zj68cG4bcaA/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). 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
Re: [Freesurfer] Freesurfer- subcortical group analysis
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 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 > *Sent:* 27 May 2021 21:05 > *To:* Aldinhas De Freitas Ferreira, Francisca > > *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 > . 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://secure-web.cisco.com/1aa2SiyojiXB68BwDW7pBUi7Bb4E8YBIfrdOl8sVnGWmr6BlEbaLwyxvb5f_rl2R1l8oteCMESQ19CyPzF7bmRkoDLHH5iTRJ6ALAwpEhJThFidJmMawaOw9Jg6GVBTgWRyeTqv_YG5vwBRZ6kENBM_78wuDd4yG_SKTe7lqNtQZACz6lN-59GaDUAJw_nlLFaY_eGOByASaU
