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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
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:
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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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 CautionDear 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
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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:
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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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Douglas N. Greve -
Mingyang Xia