Re: [Freesurfer] white matter volume
External Email - Use Caution If that's the correct way to do it then yes since I don't know about this. If not, is the volume of white matter obtained from freesurfers glmfit group analyses? On Tue, Feb 2, 2021 at 11:39 AM Douglas N. Greve wrote: > sorry, still don't understand. do you want to get the volume of WM from > DTI? > > On 2/2/2021 11:19 AM, Sara Lyn wrote: > > External Email - Use Caution > Hi Dr Greve, > > Instead of using DTI to get at the FA/MD etc measures is there a way to > get at the volume of the white matter? > > Best, > Sara > > On Tue, Feb 2, 2021 at 10:54 AM Douglas N. Greve > wrote: > >> Not sure what you mean >> >> On 2/1/2021 12:32 PM, Sara Lyn wrote: >> >> External Email - Use Caution >> Hi, >> >> Is there a way to get at the white matter volume from a group analysis? >> >> Sara >> >> ___ >> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1mFhEizu4Fx-vZ0Cn8uHzkNGSCaMMFACs4pDOVxupD9yud98dsA6MG_BtyxgPpvhWKsLySWrrAOreJMoBwyQ0UZ8MCbjCUz7d7XC-2X3i2xMCWyAcLAsTIC_P6qfQ8p24t5fK15SrlcU4kwXKumjpTBCrXUKmt-mhwarJF2Am7A4duXq0JS4hJXwKXHkOqIetSBhSApQLHh2ZjRQ6z80XBD1SyiQ51Ow9HNBu4D8ekgUix8j-Ik1ahcYhhe30r4pghx7Hm6FSeg27Vi0DBQ279g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1nxIWaZHNI7xNtv85vkNHiK2rzIYpWyRgsNK2sYLfcAoTWyH4nSJEVLRGcnHxr97Vi8Icr7uk_oFxUBPO0I8nlD9KwcNgX2mqq6yOIpJTVpx76geIQXuhPKliIL2KOV4b00z3LD_75LfkmM2ZREsai9hWUYqz1iSv77kQETpj-4XkQRPDdIIfi2W2jkOdvssNCWywGAF6e111YdqjKm0HtYMVI4CYBjFFvE8Tk_60tVQehASKha2zqOWVuQlCD2mdfUxbiuyc6UfRMC7wuRWH_Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1mFhEizu4Fx-vZ0Cn8uHzkNGSCaMMFACs4pDOVxupD9yud98dsA6MG_BtyxgPpvhWKsLySWrrAOreJMoBwyQ0UZ8MCbjCUz7d7XC-2X3i2xMCWyAcLAsTIC_P6qfQ8p24t5fK15SrlcU4kwXKumjpTBCrXUKmt-mhwarJF2Am7A4duXq0JS4hJXwKXHkOqIetSBhSApQLHh2ZjRQ6z80XBD1SyiQ51Ow9HNBu4D8ekgUix8j-Ik1ahcYhhe30r4pghx7Hm6FSeg27Vi0DBQ279g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1nxIWaZHNI7xNtv85vkNHiK2rzIYpWyRgsNK2sYLfcAoTWyH4nSJEVLRGcnHxr97Vi8Icr7uk_oFxUBPO0I8nlD9KwcNgX2mqq6yOIpJTVpx76geIQXuhPKliIL2KOV4b00z3LD_75LfkmM2ZREsai9hWUYqz1iSv77kQETpj-4XkQRPDdIIfi2W2jkOdvssNCWywGAF6e111YdqjKm0HtYMVI4CYBjFFvE8Tk_60tVQehASKha2zqOWVuQlCD2mdfUxbiuyc6UfRMC7wuRWH_Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > ___ > 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/1mFhEizu4Fx-vZ0Cn8uHzkNGSCaMMFACs4pDOVxupD9yud98dsA6MG_BtyxgPpvhWKsLySWrrAOreJMoBwyQ0UZ8MCbjCUz7d7XC-2X3i2xMCWyAcLAsTIC_P6qfQ8p24t5fK15SrlcU4kwXKumjpTBCrXUKmt-mhwarJF2Am7A4duXq0JS4hJXwKXHkOqIetSBhSApQLHh2ZjRQ6z80XBD1SyiQ51Ow9HNBu4D8ekgUix8j-Ik1ahcYhhe30r4pghx7Hm6FSeg27Vi0DBQ279g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] white matter volume
External Email - Use Caution Hi Dr Greve, Instead of using DTI to get at the FA/MD etc measures is there a way to get at the volume of the white matter? Best, Sara On Tue, Feb 2, 2021 at 10:54 AM Douglas N. Greve wrote: > Not sure what you mean > > On 2/1/2021 12:32 PM, Sara Lyn wrote: > > External Email - Use Caution > Hi, > > Is there a way to get at the white matter volume from a group analysis? > > Sara > > ___ > 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/1nxIWaZHNI7xNtv85vkNHiK2rzIYpWyRgsNK2sYLfcAoTWyH4nSJEVLRGcnHxr97Vi8Icr7uk_oFxUBPO0I8nlD9KwcNgX2mqq6yOIpJTVpx76geIQXuhPKliIL2KOV4b00z3LD_75LfkmM2ZREsai9hWUYqz1iSv77kQETpj-4XkQRPDdIIfi2W2jkOdvssNCWywGAF6e111YdqjKm0HtYMVI4CYBjFFvE8Tk_60tVQehASKha2zqOWVuQlCD2mdfUxbiuyc6UfRMC7wuRWH_Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical thickness ROI
External Email - Use Caution Hi Freesurfer developers, I wanted to know if I could use an ROI obtained from cortical thickness group analysis to obtain FA values from that same ROI for each of the subjects. Appreciate any guidance, thank you. Sincerely, Sara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] white matter volume
External Email - Use Caution Hi, Is there a way to get at the white matter volume from a group analysis? Sara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] group analyses {Disarmed}
External Email - Use Caution And also i'm trying to extract these values from the uncorrected maps not corrected. Is there a way for that? Thank you On Mon, Dec 14, 2020 at 9:59 AM Sara Lyn wrote: > Hi > Thank you for your response. How do I correct this extracted volume for > intracranial volume (etiv)? > > Thank you > > Sara > > On Sun, Dec 13, 2020 at 12:30 PM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > >> When you run the thickness analysis with multiple comparisons correction >> (mri_glmfit-sim), it will create "ocn" files. These will be clusters of the >> significant areas. You can use this to extract other information. If you >> want volume, then run mris_preproc using the --meas volume flag, the apply >> the ocn to this file using mri_segstats using the --avgwf and --accumulate >> flags (and --exclude 0). This will give you a nsubjects-by-nclusters text >> file where each entry is the volume for that subject/cluster >> >> On 12/8/2020 10:48 AM, Sara Lyn wrote: >> >> External Email - Use Caution >> Hi Joceyln, >> >> I'm not trying to run a new group analysis but want to extract volume >> values from significant thickness ROIs obtained from a thickness >> group analysis. >> >> Thank you >> >> Sara >> >> On Tue, Dec 8, 2020 at 10:38 AM Mora, Jocelyn S. >> wrote: >> >>> Hi Sara, >>> >>> You may want to try --meas volume in place of --meas thickness when >>> running mris_preproc. >>> >>> I would also recommend looking at our ROI Analysis >>> <https://secure-web.cisco.com/1g2kRJfau7HjSgmWu9k1y2XTwIMcBGIA-XwH0H7VI8zAxTQzb4aOSMDp6R8Jfi0Po3NMRSG9C0LtNtm6-woQEgwl-cwbWL8_TXyPMqoIvev2Gk5xKmwgW8IuFaQjw69Y3FCuRKwDVHOMSTjPP3MAi29ARxwq_LRpLO7bxtHZW1jAyuRNtrmD4erpddTzuHg3F62ADZRqOYBLyWHlzBBPqp7yCdVoH4o7Gia01u1hT-aoNc8JHUlKMud7cMQz4MsOZAOv64wbXgkh8bAUP0bhvAg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROIV6.0> >>> tutorial and Volumetric Group Analysis >>> <https://secure-web.cisco.com/1tHYiEwJMSx00y8RdQYJIg0nUV5bkFIzrk567zMxayemPQ09G48rqDnWqw4E6yrlMBJLktsyeyMdqA8GdbPJDzXQF7xx_UyMd7vKwH4Re9TF4tJdv1FaNzemfK7i5QI7Psfkt891h5PytK7i7KSod464UAFFriIC4NrIYk_lzZGh6ljc-y-Q3jIxXf0RbP6lDllgUJaJ3XS9i_BCSUoZAUhpAyzrfLoi1XWxtXjxQl_iCBoocEJOpE_SFyFHLaZYUyWgGShrqcIZTYr-w7rqWSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FVolumetricGroupAnalysis%3Fhighlight%3D%2528thickness%2529%257C%2528volume%2529%257C%2528measure%2529> >>> tutorial. Please let us know if you are still having trouble. >>> >>> Cheers, >>> Jocelyn >>> -- >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sara Lyn < >>> saralyn...@gmail.com> >>> *Sent:* Monday, December 7, 2020 10:43 AM >>> *To:* Freesurfer support list >>> *Subject:* [Freesurfer] group analyses >>> >>> >>> External Email - Use Caution >>> Hi FS developers, >>> >>> I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte >>> carlo) for a surface based thickness group analysis. I am trying to extract >>> volume measures from the same significant thickness ROIs. Is there any way >>> to do this? Thank you! >>> >>> Sara >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/1u1qt6A_p-tSrIcM3Ob-eaA-qgeLYw5E0lUOmdAR_bR0uNqYVCHp2018ZnUjxx4v4g73ubLNxzODe3YS83Po3nv7CLS4xB_iu53eGb3qd5m7vBvR7oUpBirosANCNaOIO0LXEBukkqYl4wz4vxD22r-p6aegqPfd3L6gFj0tbXGVpO_Cnz7_I9nXILpZDiJa4JwUIMXJjPtn0reUNRLJAzvhEOaOM8SM-y9JL5fVZe-4RTaNwekw3PkDx2zZlh1OJNWfVJXhl9Y4sNQFq0F_kWQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <https://secure-web.cisco.com/1R7gYfs8YU2juqb8rGfBqpwv3CspfKQQgYn6WAikOwc_TDtnxjDjMy1r78KDcMil_IHVde58fWtF5nHDeV6y8sFImL3Jlld9a57iSW_DaW4BFEV6cg_YjqRNhnbaF-4ZaZFCs50k7MRt2-YvVF4mZuaP6kh5g9RnM5y_TMYZJm0LyS8ruzjLF6IgU9yMOHVXmVHUWva7T8KfHrZiljMRns81fwr4TsXqvlnzXZDMISe0Rk2ANRklyDOi8QKTcN8ierog6gWIQQPYLNQce_Kn_gw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> __
Re: [Freesurfer] group analyses {Disarmed}
External Email - Use Caution Hi Thank you for your response. How do I correct this extracted volume for intracranial volume (etiv)? Thank you Sara On Sun, Dec 13, 2020 at 12:30 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > When you run the thickness analysis with multiple comparisons correction > (mri_glmfit-sim), it will create "ocn" files. These will be clusters of the > significant areas. You can use this to extract other information. If you > want volume, then run mris_preproc using the --meas volume flag, the apply > the ocn to this file using mri_segstats using the --avgwf and --accumulate > flags (and --exclude 0). This will give you a nsubjects-by-nclusters text > file where each entry is the volume for that subject/cluster > > On 12/8/2020 10:48 AM, Sara Lyn wrote: > > External Email - Use Caution > Hi Joceyln, > > I'm not trying to run a new group analysis but want to extract volume > values from significant thickness ROIs obtained from a thickness > group analysis. > > Thank you > > Sara > > On Tue, Dec 8, 2020 at 10:38 AM Mora, Jocelyn S. > wrote: > >> Hi Sara, >> >> You may want to try --meas volume in place of --meas thickness when >> running mris_preproc. >> >> I would also recommend looking at our ROI Analysis >> <https://secure-web.cisco.com/1g2kRJfau7HjSgmWu9k1y2XTwIMcBGIA-XwH0H7VI8zAxTQzb4aOSMDp6R8Jfi0Po3NMRSG9C0LtNtm6-woQEgwl-cwbWL8_TXyPMqoIvev2Gk5xKmwgW8IuFaQjw69Y3FCuRKwDVHOMSTjPP3MAi29ARxwq_LRpLO7bxtHZW1jAyuRNtrmD4erpddTzuHg3F62ADZRqOYBLyWHlzBBPqp7yCdVoH4o7Gia01u1hT-aoNc8JHUlKMud7cMQz4MsOZAOv64wbXgkh8bAUP0bhvAg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROIV6.0> >> tutorial and Volumetric Group Analysis >> <https://secure-web.cisco.com/1tHYiEwJMSx00y8RdQYJIg0nUV5bkFIzrk567zMxayemPQ09G48rqDnWqw4E6yrlMBJLktsyeyMdqA8GdbPJDzXQF7xx_UyMd7vKwH4Re9TF4tJdv1FaNzemfK7i5QI7Psfkt891h5PytK7i7KSod464UAFFriIC4NrIYk_lzZGh6ljc-y-Q3jIxXf0RbP6lDllgUJaJ3XS9i_BCSUoZAUhpAyzrfLoi1XWxtXjxQl_iCBoocEJOpE_SFyFHLaZYUyWgGShrqcIZTYr-w7rqWSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FVolumetricGroupAnalysis%3Fhighlight%3D%2528thickness%2529%257C%2528volume%2529%257C%2528measure%2529> >> tutorial. Please let us know if you are still having trouble. >> >> Cheers, >> Jocelyn >> -- >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sara Lyn < >> saralyn...@gmail.com> >> *Sent:* Monday, December 7, 2020 10:43 AM >> *To:* Freesurfer support list >> *Subject:* [Freesurfer] group analyses >> >> >> External Email - Use Caution >> Hi FS developers, >> >> I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte >> carlo) for a surface based thickness group analysis. I am trying to extract >> volume measures from the same significant thickness ROIs. Is there any way >> to do this? Thank you! >> >> Sara >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1Ah2pQDy0yVPBrfOlJQCt09VXbFckNrCLFlfFNhGHNiCLlihCT3a6Ao1ukmi54Op5WeEN28uVon2Aa_HTqcoHfEdsl_re_L0spoNerp7ipV9SBML8-Q3TGejLNOFiCik56W4gG1pbAWG_X1hi5bEiosvdOAY-lEqJpt5S0y7GXEuii4ROjgqTz8VOufJkTAi4noM8xExAhDNJ7pHx9On1nmsWsG2uGmkUMr-a0lvO1xexIN4H4GW4jke_tb9H5_AdIqrFbjW7k_1RzaJhTHezvg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1R7gYfs8YU2juqb8rGfBqpwv3CspfKQQgYn6WAikOwc_TDtnxjDjMy1r78KDcMil_IHVde58fWtF5nHDeV6y8sFImL3Jlld9a57iSW_DaW4BFEV6cg_YjqRNhnbaF-4ZaZFCs50k7MRt2-YvVF4mZuaP6kh5g9RnM5y_TMYZJm0LyS8ruzjLF6IgU9yMOHVXmVHUWva7T8KfHrZiljMRns81fwr4TsXqvlnzXZDMISe0Rk2ANRklyDOi8QKTcN8ierog6gWIQQPYLNQce_Kn_gw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > ___ > 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/1Ah2pQDy0yVPBrfOlJQCt09VXbFckNrCLFlfFNhGHNiCLlihCT3a6Ao1ukmi54Op5WeEN28uVon2Aa_HTqcoHfEdsl_re_L0spoNerp7ipV9SBML8-Q3TGejLNOFiCik56W4gG1pbAWG_X1hi5bEiosvdOAY-lEqJpt5S0y7GXEuii4ROjgqTz8VOufJkTAi4noM8xExAhDNJ7pHx9On1nmsWsG2uGmkUMr-a0lvO1xexIN4H4GW4jke_tb9H5_AdIqrFbjW7k_1RzaJhTHezvg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] group analyses {Disarmed}
External Email - Use Caution Hi Joceyln, I'm not trying to run a new group analysis but want to extract volume values from significant thickness ROIs obtained from a thickness group analysis. Thank you Sara On Tue, Dec 8, 2020 at 10:38 AM Mora, Jocelyn S. wrote: > Hi Sara, > > You may want to try --meas volume in place of --meas thickness when > running mris_preproc. > > I would also recommend looking at our ROI Analysis > <https://secure-web.cisco.com/1g2kRJfau7HjSgmWu9k1y2XTwIMcBGIA-XwH0H7VI8zAxTQzb4aOSMDp6R8Jfi0Po3NMRSG9C0LtNtm6-woQEgwl-cwbWL8_TXyPMqoIvev2Gk5xKmwgW8IuFaQjw69Y3FCuRKwDVHOMSTjPP3MAi29ARxwq_LRpLO7bxtHZW1jAyuRNtrmD4erpddTzuHg3F62ADZRqOYBLyWHlzBBPqp7yCdVoH4o7Gia01u1hT-aoNc8JHUlKMud7cMQz4MsOZAOv64wbXgkh8bAUP0bhvAg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROIV6.0> > tutorial and Volumetric Group Analysis > <https://secure-web.cisco.com/1tHYiEwJMSx00y8RdQYJIg0nUV5bkFIzrk567zMxayemPQ09G48rqDnWqw4E6yrlMBJLktsyeyMdqA8GdbPJDzXQF7xx_UyMd7vKwH4Re9TF4tJdv1FaNzemfK7i5QI7Psfkt891h5PytK7i7KSod464UAFFriIC4NrIYk_lzZGh6ljc-y-Q3jIxXf0RbP6lDllgUJaJ3XS9i_BCSUoZAUhpAyzrfLoi1XWxtXjxQl_iCBoocEJOpE_SFyFHLaZYUyWgGShrqcIZTYr-w7rqWSQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FVolumetricGroupAnalysis%3Fhighlight%3D%2528thickness%2529%257C%2528volume%2529%257C%2528measure%2529> > tutorial. Please let us know if you are still having trouble. > > Cheers, > Jocelyn > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sara Lyn < > saralyn...@gmail.com> > *Sent:* Monday, December 7, 2020 10:43 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] group analyses > > > External Email - Use Caution > > Hi FS developers, > > I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte > carlo) for a surface based thickness group analysis. I am trying to extract > volume measures from the same significant thickness ROIs. Is there any way > to do this? Thank you! > > Sara > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1R7gYfs8YU2juqb8rGfBqpwv3CspfKQQgYn6WAikOwc_TDtnxjDjMy1r78KDcMil_IHVde58fWtF5nHDeV6y8sFImL3Jlld9a57iSW_DaW4BFEV6cg_YjqRNhnbaF-4ZaZFCs50k7MRt2-YvVF4mZuaP6kh5g9RnM5y_TMYZJm0LyS8ruzjLF6IgU9yMOHVXmVHUWva7T8KfHrZiljMRns81fwr4TsXqvlnzXZDMISe0Rk2ANRklyDOi8QKTcN8ierog6gWIQQPYLNQce_Kn_gw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] group analyses
External Email - Use Caution Hi FS developers, I ran mris_preproc, surf2 surf and glmfit and cluster analyses (monte carlo) for a surface based thickness group analysis. I am trying to extract volume measures from the same significant thickness ROIs. Is there any way to do this? Thank you! Sara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
External Email - Use Caution Hi Freesurfer experts, I'm doing a surface based volume analysis and wanted to know if there was a flag to regress out eTIV in the model. Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Group Analysis {Disarmed}
External Email - Use Caution Hi Jocelyn, The links talk about measuring thickness and I’m trying to do a volumetric Group analysis using Glm. I was wondering if you could point me towards that. Sara On Thursday, November 19, 2020, Mora, Jocelyn S. wrote: > Hi Sara, > > You may want to use asegstats2table. Follow these links to learn more > about mris_preproc, mri_glmfit, and asegstats2table: > > http://secure-web.cisco.com/1GcyAZ4TLbRGiuwf3mK0o8IKvcNsxwTULArjRsgQ5-qwwWHseO7Av6RqT8xdhHsL8LHTuIoRLCNHWJBGJo8Agt99_QoT95gst9PbZMUpV2KB70uY9UQ9u_d_-hUpKT_FeCzOVvl_lfE4h9bW6yCb5jjb1LQ_MU8B1aU-8LZ-rOZ3Z_UxUqD99IHmZtQtuT3AfjYAQtdNUl3Y-k3Wh8Cxo4TeJbHILfSoBj3GfcLaPCha4Lkm7H-FDht547FiGBuaBs8Z7W9kOgEGho_vHNXh8yQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_preproc > > https://secure-web.cisco.com/1OylzWdn9KNXiaXZXnAXy6Y4zKLT3o_SWqfBObqbSeLwwdc8tsdpFt2tbgaY-ZpE74DE_FWqKA1H-7VuWM-jYEKTZp-Ny65io8jvj--7yeL73z9eRk3xlO93UaGBNsja6Sa3X8M_0B6S9ue1xUjhCdq4rEU32tzHnrDZAmbSDQau-qb-nqAw-nWHhqMzuidDzkRMr-r4lJoacIJgr64ig_TueonRzEASSPIyGdi-lTXBy5Jj-XHWqBskYmql34McxnPTEJ_yEr96CR9Gqm2nCHg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_glmfit? > highlight=%28asegstats%29 > > https://secure-web.cisco.com/1v3oCpx-Uv895Hjxj-klxnZ5JfvSWRtw-oWz6bxIOFQbCONpO8RheJdg0dRyqYZa4PqaDfJc8acNicFvz5R9bSncZdGGbhCfB6yVa7_6KwYtN9lbb0OupYLTxrLYqiTx2HjlXsbpppU1LruUY4s3JEhSc_hQvATe7qGevs5lDVwCtMTxRVVn2OJXGL3abOdjKN-yG1KE_hL5frEdisidhiiPH9TxCvNFa0TLbAOsM4s7GmxLy5P5fTUvxHL-O9jtRMg3oNmO_qppP5uvufABpjw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fasegstats2table%3Fhighlight%3D%25 > 28asegstats%29 > > Best, > Jocelyn > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sara Lyn < > saralyn...@gmail.com> > *Sent:* Wednesday, November 18, 2020 6:37 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Group Analysis > > > External Email - Use Caution > > Hi Freesurfer experts, > > I was looking to run the three steps of group analysis-mris preproc, mri > surf2surf using the measure volume and unsure of how to go about it since > the wiki page talks about thickness only. I would appreciate any help. > > Best, > Sara > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Group Analysis
External Email - Use Caution Hi Freesurfer experts, I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help. Best, Sara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] MRI_seg stats for multiple subjects
External Email - Use Caution
Hi freesurfer developers,
I am trying to run mri segstats for multiple subjects but the following
only produces one text file for the first subject. Any idea what I am doing
wrong?
for subj in $(cat sessid.txt); do
mri_segstats --seg
/Users/Desktop/AUT/dti/TBSS_FA/FA/${subj}_FA_skeleton_JHU_wmparc_segmentation.nii.gz
--in /Users/Desktop/AUT/dti/TBSS_FA/origdata/${subj}.nii.gz --ctab
/Users/Desktop/AUT/TBSS_FA/stats/JHU_wmparc_segmentation_ColorLUT.txt
--sum /Users/Desktop/AUT/TBSS_FA/roi/FA_${subj}_M.txt
done
Thank you.
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[Freesurfer] Atlas question
External Email - Use Caution Hi FS developers I'm doing an ROI analysis with data data and was wondering if there exists a merged Freesurfer white matter parcellation and Johns Hopkins University white matter label atlas. If yes what is it called and where can I find it? I am trying to label the mean FA skeleton mao with this merged atlas and then deproject it to subjects native space. Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
