If all you want is the mean time course from hippocampus, there is an easier/better way, eg
First, create a configuration that describes the ROI you want, eg, fcseed-config -segid 17 -fcname L_Hippo.dat -fsd bold -mean -cfg mean.L_Hippo.config This is done once regardless of how many subjects you have Then for each subject, run fcseed-sess -s sessionid -cfg L_Hippo.config This will create L_Hippo.dat in each run folder Note that "17" comes from $FREESURFER_HOME/FreeSurferColorLUT.txt
On 6/1/2022 1:41 PM, Mingyang Xia wrote:
External Email - Use Caution
Dear freesurfer expert: I use freesurfer to preprocess the fmri signal. It generates three final files: fmcpr.up.sm5.fsaverage.lh.nii.gz, fmcpr.up.sm5.fsaverage.rh.nii.gz, and fmcpr.up.sm5.mni305.2. However I want to extract the subcortical area signal, for example the signal on the hippocampus. How could I extract the signal in the subcortical areas and find their labels and corresponding files? Thank you Mingyang
On Tue, May 31, 2022 at 8:16 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
what do you man by the label of the file? If you want a mask, there should be a mask in the mask folder On 5/23/2022 10:05 PM, Mingyang Xia wrote:External Email - Use Caution Dear Freesurfer expert: I am Mingyang Xia. I use freesurfer to preprocess the fmri data and map to the fsaverage and generate a file named fmcpr.up.sm5.mni305.2mm.nii.gz. I want to get the label of this file however I could not find the label in the fsaverage folder. Could you give me some advice? Thank you Mingyang Xia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1BNL93VBTxkINpOJLmbPjUq_8EbNjR2oQeHswbDqY9VuKtT__KT9QzQOWc7YcLkPRbeznyUKbmFffe_vMFmCLIBmQy39YLyz6EvZjNFCXwqhARjZGGIyNB6rra4g6Q8CjHgOW1klJ8zPr7ZFDTucIWsVuyR6AxB7Xsy2l24NDHXd03VyzYuK1Xp_RHJK_5HzUoIVmLnWDzap3KS6Xe7cbHN2UqjhV3eFyTFf6vN2TMdnEd8Puqwr3ZRwYjBxd1ghl1iHSZP0yRTdfvEmSY4tXge1L1i9T5MUHDL-ZquJmdr1VZvfMeEE8AvYZSB5j5ySdt7Rz7qbMyw5Wfg8wEU9veg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21LIr3w8kk_Xxm%21vWtpM8HCCIRjFLr2rlEKhbHZG_MsCo01rhbVCmDc2YWn1WVZjXGd59FAJ7CDpnLXwzLGokN0q00xBfRRiCZ_3w%24>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!LIr3w8kk_Xxm!vWtpM8HCCIRjFLr2rlEKhbHZG_MsCo01rhbVCmDc2YWn1WVZjXGd59FAJ7CDpnLXwzLGokN0q00xBfRRiCZ_3w$ <https://secure-web.cisco.com/1BNL93VBTxkINpOJLmbPjUq_8EbNjR2oQeHswbDqY9VuKtT__KT9QzQOWc7YcLkPRbeznyUKbmFffe_vMFmCLIBmQy39YLyz6EvZjNFCXwqhARjZGGIyNB6rra4g6Q8CjHgOW1klJ8zPr7ZFDTucIWsVuyR6AxB7Xsy2l24NDHXd03VyzYuK1Xp_RHJK_5HzUoIVmLnWDzap3KS6Xe7cbHN2UqjhV3eFyTFf6vN2TMdnEd8Puqwr3ZRwYjBxd1ghl1iHSZP0yRTdfvEmSY4tXge1L1i9T5MUHDL-ZquJmdr1VZvfMeEE8AvYZSB5j5ySdt7Rz7qbMyw5Wfg8wEU9veg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21LIr3w8kk_Xxm%21vWtpM8HCCIRjFLr2rlEKhbHZG_MsCo01rhbVCmDc2YWn1WVZjXGd59FAJ7CDpnLXwzLGokN0q00xBfRRiCZ_3w%24> 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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__https://www.massgeneralbrigham.org/complianceline__;!!LIr3w8kk_Xxm!vWtpM8HCCIRjFLr2rlEKhbHZG_MsCo01rhbVCmDc2YWn1WVZjXGd59FAJ7CDpnLXwzLGokN0q00xBfRflqlXRA$ <https://secure-web.cisco.com/1UVUcP3LRH-hZrHnzU83FYw8rWkxk82zPXzdEjisz02n37eMsfOiuqpEFU93Nqcksp9hSwBSsSKeO2xPoq_BYg8tH3HGHsLi-797hK6dJWRGhUPfDn7bpd7QnMTschRjYyCwsZn0Gw7G6k8GKuwk6j_JpKLdmoR5VlWB5WxrYgIjy5q0jdenoiMA5X8N_QLxmoRA4FxfheQ2V851dooEm8iqx4Mf2WsVTmbE9jVhJal0pZVFKde7dsyS8NOS0N1jN3rr853V35awT3f3qN5pX2HoCLAuqVPL0056ccrzyXpXSAhEMqhkabPnE2utEUtImw4mOqLOfikWkbsxicYXrww/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline__%3B%21%21LIr3w8kk_Xxm%21vWtpM8HCCIRjFLr2rlEKhbHZG_MsCo01rhbVCmDc2YWn1WVZjXGd59FAJ7CDpnLXwzLGokN0q00xBfRflqlXRA%24> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://urldefense.com/v3/__https://www.massgeneralbrigham.org/complianceline__;!!LIr3w8kk_Xxm!vWtpM8HCCIRjFLr2rlEKhbHZG_MsCo01rhbVCmDc2YWn1WVZjXGd59FAJ7CDpnLXwzLGokN0q00xBfRflqlXRA$ <https://secure-web.cisco.com/1UVUcP3LRH-hZrHnzU83FYw8rWkxk82zPXzdEjisz02n37eMsfOiuqpEFU93Nqcksp9hSwBSsSKeO2xPoq_BYg8tH3HGHsLi-797hK6dJWRGhUPfDn7bpd7QnMTschRjYyCwsZn0Gw7G6k8GKuwk6j_JpKLdmoR5VlWB5WxrYgIjy5q0jdenoiMA5X8N_QLxmoRA4FxfheQ2V851dooEm8iqx4Mf2WsVTmbE9jVhJal0pZVFKde7dsyS8NOS0N1jN3rr853V35awT3f3qN5pX2HoCLAuqVPL0056ccrzyXpXSAhEMqhkabPnE2utEUtImw4mOqLOfikWkbsxicYXrww/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline__%3B%21%21LIr3w8kk_Xxm%21vWtpM8HCCIRjFLr2rlEKhbHZG_MsCo01rhbVCmDc2YWn1WVZjXGd59FAJ7CDpnLXwzLGokN0q00xBfRflqlXRA%24> > . 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.
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