External Email - Use Caution Hello Douglas,
I am afraid I am getting error while running "mris_preproc --fsgd steplengthSD_vol.fsgd" ERROR: no subjects specified I believe I am missing very basic and doing wrong while exporting specific paths and subject names. Could you please help to resolve the issue? I am working on bash shell. So, I first ran <source_freesurfer>. like the following export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl All my 'recon-all -all -qcache' data are kept in /usr/local/freesurfer/subjects. I have created a folder 'glm' here and transferred all the data. I have also created.fsgd and .mtx file and saved them inside the 'glm' folder. So, next two steps I did- export SUBJECTS_DIR=/usr/local/freesurfer/subjects cd $SUBJECTS_DIR/glm Thank you for your time and help. Regards, KC On Mon, Feb 14, 2022 at 10:48 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > Yes, single group just means a single class in the FSGD file. Then just > include your clinical measure as a variable in the FSGD > > On 2/14/2022 11:39 AM, Koustav Chatterjee wrote: > > External Email - Use Caution > Thanks. > I am afraid since I am working on a single group ( only patient group), > can I run the same? > > On Mon, 14 Feb, 2022, 9:51 pm Douglas N. Greve, <dgr...@mgh.harvard.edu> > wrote: > >> You can run a group analysis >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1rRbPK8Ag291KHeTtdIMQM42oPAVg-pl1Ee4UYnkQ4czZh0Cqw9ym6yDwJfF4g3p7Me3WHtD4PADqZU0V1YnNUeVpNsv0ViKUUd2ihQZ6RBTurqLhEKQ5GjsY5MDqxE5zbGeCc0TrP2d_NGG5KnJUI3i4YrpXBAqc0ACrZzksh6FNWPDTJnVXz2GSbxO8lcyM2uyuWgqPdtn4tAinZmQQY_nz8KMcbYrvZPLPUeaS9NLmQoi1of9ubw1WGSzuRwHYh0pZOsSpNsd-qSH7r-oxJ4KDHvGE6l104y1vSthS0XG32tiKPFDP9kjx8YlwCH86OnU5d-iGg5gJsXjtJEAlGg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis >> <https://secure-web.cisco.com/1Ff-dG17xkRm3OY5bDYlwFveyhE5l-WyDkWe_cFQyvOPXWqZtusTfsRPvlPr3yJR_a7H0wxgFYw-HsZJFFWr-500I3mRgVJO3GhgT_MzGifPJZXW4OVwN0rpx8Mi51yAC41a-Uihdgf0OE_F8EJ1o4oInwE8B6GJjH_Y6fFTZ0QBGnKj2UFByxPmtaXUAu-5-whHQd7ix5RLtWdRXuhRwZAHKyITK2bG_iOoUR7UBm5dK0M2bP4LV6x92HJGYCw_oJGhpL8tvMhl8UeAmtCU9deV3FLuLoTBkSvHw0-5NJAAQuiJYK1gyeuU3norr7mIYPeZ6qkyiBP0topWayXXHTg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis> >> One of the outputs will be the correlation (along with the sig of the >> correlation) >> >> >> On 2/13/2022 6:35 PM, Koustav Chatterjee wrote: >> >> External Email - Use Caution >> Dear FreeSurfer experts, >> >> I am trying to find the correlation between the regional cortical >> thickness and volume with different clinical measures of a >> neurodegenerative condition. I am using DK atlas to get the cortical >> measures and establish the correlation using SPSS, a statistical software. >> >> But, I would like to get FreeSurfer developed images. I would like to >> learn how to get the areas through images (the FreeSurfer pipeline >> generated images showing brain regions associated with clinical measures I >> am interested in). >> >> Looking for your kind help. >> >> Regards, >> KC >> >> _______________________________________________ >> 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/1vQwXqNPiE3wE9rcRkdbs_n20_x6bWGvTn0zOvNjaVmHJnNnGtvv0HcFEAyc3rbkZ_qgQYhzG9exaAuwV4UnAZP1cncAOExBANDKUpUEmgeCqh1fpZfqFvm2PZHbRLkk7sQwGU7OONtwAxLVGax9dLkB79Um1E15ZguEJ4wsljruAdw54hMKhM6vBhPsbi6UdAfr0qdwwzc1mRmfpeviONV32Xc3AQ_J46LDTvCU9YANl6dC9339srgQkDSlgbQ-0MO7HUzvTOELXYyy9GhEO5Y8YB-wSyDXrnm_AwgID1WXF-WIWlJPTKp240VuFl80lFKGwuQGRimEfL5J4HJSqJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1vmI2rQNZhXFW1eSQ50tThABmAXKnIkegT3FEjChe5oy0YfRN9qSvq1heX8tLBV6_YgS70TxxUk2qDYJEDjZAWbzc44AinVPSYX-IUWAYWzqaCGzgqcfC0yDy5htaDCtbvRqom9zOtJl41o9DNRgBZopDt-twGierCA-LmhditLTvENqU2PjBo6FUnPj8XTc-bPQtcP5wUtiYLLRAAzNcF4JDHhBc8tDmDcQxTDzA3aSiaImM3vs5mdExCyarv21uPkcw-cHN1En21nkax_b2Dxu_lk7mYQWBJE5667jUSJdYWO3NGOTceCuOjDVUJQ63bQ6x1MK99DKRj7BZhK5tog/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/1vQwXqNPiE3wE9rcRkdbs_n20_x6bWGvTn0zOvNjaVmHJnNnGtvv0HcFEAyc3rbkZ_qgQYhzG9exaAuwV4UnAZP1cncAOExBANDKUpUEmgeCqh1fpZfqFvm2PZHbRLkk7sQwGU7OONtwAxLVGax9dLkB79Um1E15ZguEJ4wsljruAdw54hMKhM6vBhPsbi6UdAfr0qdwwzc1mRmfpeviONV32Xc3AQ_J46LDTvCU9YANl6dC9339srgQkDSlgbQ-0MO7HUzvTOELXYyy9GhEO5Y8YB-wSyDXrnm_AwgID1WXF-WIWlJPTKp240VuFl80lFKGwuQGRimEfL5J4HJSqJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1vmI2rQNZhXFW1eSQ50tThABmAXKnIkegT3FEjChe5oy0YfRN9qSvq1heX8tLBV6_YgS70TxxUk2qDYJEDjZAWbzc44AinVPSYX-IUWAYWzqaCGzgqcfC0yDy5htaDCtbvRqom9zOtJl41o9DNRgBZopDt-twGierCA-LmhditLTvENqU2PjBo6FUnPj8XTc-bPQtcP5wUtiYLLRAAzNcF4JDHhBc8tDmDcQxTDzA3aSiaImM3vs5mdExCyarv21uPkcw-cHN1En21nkax_b2Dxu_lk7mYQWBJE5667jUSJdYWO3NGOTceCuOjDVUJQ63bQ6x1MK99DKRj7BZhK5tog/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/1vQwXqNPiE3wE9rcRkdbs_n20_x6bWGvTn0zOvNjaVmHJnNnGtvv0HcFEAyc3rbkZ_qgQYhzG9exaAuwV4UnAZP1cncAOExBANDKUpUEmgeCqh1fpZfqFvm2PZHbRLkk7sQwGU7OONtwAxLVGax9dLkB79Um1E15ZguEJ4wsljruAdw54hMKhM6vBhPsbi6UdAfr0qdwwzc1mRmfpeviONV32Xc3AQ_J46LDTvCU9YANl6dC9339srgQkDSlgbQ-0MO7HUzvTOELXYyy9GhEO5Y8YB-wSyDXrnm_AwgID1WXF-WIWlJPTKp240VuFl80lFKGwuQGRimEfL5J4HJSqJA/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
