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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 dgreve@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 CautionThanks. 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, dgreve@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-pl1Ee4UYnkQ4czZh0... 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 CautionDear 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
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