Dear experts,
I have two questions about hemisphere analysis:
1) When I run left-right hemisphere paired t-test, can I add age as covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table? 2) I want to reorganize the hemisphere from left-right to symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it?
Thanks for your patient and help.
All best, Lanbo Wang
On 11/06/2017 12:03 PM, lanbo Wang wrote:
Dear experts,
I have two questions about hemisphere analysis:
- When I run left-right hemisphere paired t-test, can I add age as
covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table?
use this one-group, one-covariate example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
- I want to reorganize the hemisphere from left-right to
symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it?
Yes, though it is a little tricky with multiple ways, each complicated in its own way. 1. Create your own design matrix. You can use the one created by mri_glmfit to start. Assuming you want symptomHemi-nosymptomHemi, then, in each subject whose symptomHemi is rh, multiply its line in the design matrix by -1. Then pass this design matrix to mri_glmfit with --X instead of passing an FSGD file. 2. Load the output of mris_preproc into matlab, eg, y = MRIread('y.mgh');, then change the sign as in #1 above, eg, y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable subject. Then save the data with MRIwrite(y,'new.y.mgh');, then run mri_glmfit as normal with the new file. 3. Run mris_preproc for each subject separately to generate an lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the sign as in #1 above with fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o lh.lh-rh.thickness.sm00.subject10.mgh Then run mri_concat to concatenate all the subjects together in the same order as they are listed in the FSGD file, then use this stack as input the mri_glmfit
Thanks for your patient and help.
All best, Lanbo Wang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear FDs,
I encountered an odd situation:
My free surfer will always shut down when I run command.
My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel Core i5
I don’t know if the compatibility is fine with my download version (MacOS Lion OS X 10.7 (64b intel)Stable v6.0.0)
Please kindly suggest.
Thanks ver much
Best Regards, Danny Deng
On Nov 7, 2017, at 7:14 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
On 11/06/2017 12:03 PM, lanbo Wang wrote:
Dear experts,
I have two questions about hemisphere analysis:
- When I run left-right hemisphere paired t-test, can I add age as
covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table?
use this one-group, one-covariate example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
- I want to reorganize the hemisphere from left-right to
symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it?
Yes, though it is a little tricky with multiple ways, each complicated in its own way.
- Create your own design matrix. You can use the one created by
mri_glmfit to start. Assuming you want symptomHemi-nosymptomHemi, then, in each subject whose symptomHemi is rh, multiply its line in the design matrix by -1. Then pass this design matrix to mri_glmfit with --X instead of passing an FSGD file. 2. Load the output of mris_preproc into matlab, eg, y = MRIread('y.mgh');, then change the sign as in #1 above, eg, y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable subject. Then save the data with MRIwrite(y,'new.y.mgh');, then run mri_glmfit as normal with the new file. 3. Run mris_preproc for each subject separately to generate an lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the sign as in #1 above with fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o lh.lh-rh.thickness.sm00.subject10.mgh Then run mri_concat to concatenate all the subjects together in the same order as they are listed in the FSGD file, then use this stack as input the mri_glmfit
Thanks for your patient and help.
All best, Lanbo Wang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I have no idea what that means. can you explain?
On 11/7/17 12:02 AM, Danny Deng wrote:
Dear FDs,
I encountered an odd situation:
My free surfer will always shut down when I run command.
My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel Core i5
I don’t know if the compatibility is fine with my download version (MacOS Lion OS X 10.7 (64b intel)Stable v6.0.0)
Please kindly suggest.
Thanks ver much
Best Regards, Danny Deng
On Nov 7, 2017, at 7:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 11/06/2017 12:03 PM, lanbo Wang wrote:
Dear experts,
I have two questions about hemisphere analysis:
- When I run left-right hemisphere paired t-test, can I add age as
covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table?
use this one-group, one-covariate example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
- I want to reorganize the hemisphere from left-right to
symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it?
Yes, though it is a little tricky with multiple ways, each complicated in its own way.
- Create your own design matrix. You can use the one created by
mri_glmfit to start. Assuming you want symptomHemi-nosymptomHemi, then, in each subject whose symptomHemi is rh, multiply its line in the design matrix by -1. Then pass this design matrix to mri_glmfit with --X instead of passing an FSGD file. 2. Load the output of mris_preproc into matlab, eg, y = MRIread('y.mgh');, then change the sign as in #1 above, eg, y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable subject. Then save the data with MRIwrite(y,'new.y.mgh');, then run mri_glmfit as normal with the new file. 3. Run mris_preproc for each subject separately to generate an lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the sign as in #1 above with fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o lh.lh-rh.thickness.sm00.subject10.mgh Then run mri_concat to concatenate all the subjects together in the same order as they are listed in the FSGD file, then use this stack as input the mri_glmfit
Thanks for your patient and help.
All best, Lanbo Wang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Danny
you need to give us more information if you want us to help you. Please include the command you ran and the entire screen output.
cheers Bruce
On Tue, 7 Nov 2017, Danny Deng wrote:
Dear FDs, I encountered an odd situation:
My free surfer will always shut down when I run command.
My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel Core i5
I don’t know if the compatibility is fine with my download version (MacOS Lion OS X 10.7 (64b intel)Stable v6.0.0)
Please kindly suggest.
Thanks ver much
Best Regards,Danny Deng
On Nov 7, 2017, at 7:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:On 11/06/2017 12:03 PM, lanbo Wang wrote: Dear experts,
I have two questions about hemisphere analysis: 1) When I run left-right hemisphere paired t-test, can I add age as covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table?use this one-group, one-covariate example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V 2) I want to reorganize the hemisphere from left-right to symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it?
Yes, though it is a little tricky with multiple ways, each complicated in its own way.
- Create your own design matrix. You can use the one created by
mri_glmfit to start. Assuming you want symptomHemi-nosymptomHemi, then, in each subject whose symptomHemi is rh, multiply its line in the design matrix by -1. Then pass this design matrix to mri_glmfit with --X instead of passing an FSGD file. 2. Load the output of mris_preproc into matlab, eg, y = MRIread('y.mgh');, then change the sign as in #1 above, eg, y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable subject. Then save the data with MRIwrite(y,'new.y.mgh');, then run mri_glmfit as normal with the new file. 3. Run mris_preproc for each subject separately to generate an lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the sign as in #1 above with fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o lh.lh-rh.thickness.sm00.subject10.mgh Then run mri_concat to concatenate all the subjects together in the same order as they are listed in the FSGD file, then use this stack as input the mri_glmfit
Thanks for your patient and help. All best, Lanbo Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Douglas,
Thanks for your reply. I created the fsgd file as you show me, and run code like this. Am I right? 1. mris_preproc --fsgd Subject.xhemi.dat \ --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.age.sm00.mgh \ --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s subj_12_1 --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s subj_22_1 --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s subj_29_1 --s subj_32_1
2. mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir glm.lh.lh-rh.thickness.age.sm10 \ --fsgd Subject.xhemi.dat \ --C Avg-thickness-age-Cor.mtx \ --surf fsaverage_sym lh
Attachment is fsgd and Avg-thickness-age-cor.mtx.
All best, Lanbo Wang
On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Danny
you need to give us more information if you want us to help you. Please include the command you ran and the entire screen output.
cheers Bruce
On Tue, 7 Nov 2017, Danny Deng wrote:
Dear FDs,
I encountered an odd situation:
My free surfer will always shut down when I run command.
My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel Core i5
I don’t know if the compatibility is fine with my download version (MacOS Lion OS X 10.7 (64b intel)Stable v6.0.0)
Please kindly suggest.
Thanks ver much
Best Regards,Danny Deng
On Nov 7, 2017, at 7:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
On 11/06/2017 12:03 PM, lanbo Wang wrote: Dear experts,
I have two questions about hemisphere analysis: 1) When I run left-right hemisphere paired t-test, can I add age as covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table?use this one-group, one-covariate example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V 2) I want to reorganize the hemisphere from left-right to symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it?
Yes, though it is a little tricky with multiple ways, each complicated in its own way.
- Create your own design matrix. You can use the one created by
mri_glmfit to start. Assuming you want symptomHemi-nosymptomHemi, then, in each subject whose symptomHemi is rh, multiply its line in the design matrix by -1. Then pass this design matrix to mri_glmfit with --X instead of passing an FSGD file. 2. Load the output of mris_preproc into matlab, eg, y = MRIread('y.mgh');, then change the sign as in #1 above, eg, y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable subject. Then save the data with MRIwrite(y,'new.y.mgh');, then run mri_glmfit as normal with the new file. 3. Run mris_preproc for each subject separately to generate an lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the sign as in #1 above with fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o lh.lh-rh.thickness.sm00.subject10.mgh Then run mri_concat to concatenate all the subjects together in the same order as they are listed in the FSGD file, then use this stack as input the mri_glmfit
Thanks for your patient and help. All best, Lanbo Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
which method are you trying to implement? If #3, then you need to run mris_preproc separately for each subject, and then run that fscalc command
On 11/07/2017 11:33 AM, lanbo Wang wrote:
Hi Douglas,
Thanks for your reply. I created the fsgd file as you show me, and run code like this. Am I right?
mris_preproc --fsgd Subject.xhemi.dat \ --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.age.sm00.mgh \ --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s subj_12_1 --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s subj_22_1 --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s subj_29_1 --s subj_32_1
mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir glm.lh.lh-rh.thickness.age.sm10 \ --fsgd Subject.xhemi.dat \ --C Avg-thickness-age-Cor.mtx \ --surf fsaverage_sym lh
Attachment is fsgd and Avg-thickness-age-cor.mtx.
All best, Lanbo Wang
On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Danny you need to give us more information if you want us to help you. Please include the command you ran and the entire screen output. cheers Bruce On Tue, 7 Nov 2017, Danny Deng wrote: Dear FDs, I encountered an odd situation: My free surfer will always shut down when I run command. My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel Core i5 I don’t know if the compatibility is fine with my download version (MacOS Lion OS X 10.7 (64b intel)Stable v6.0.0) Please kindly suggest. Thanks ver much Best Regards,Danny Deng On Nov 7, 2017, at 7:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: On 11/06/2017 12:03 PM, lanbo Wang wrote: Dear experts, I have two questions about hemisphere analysis: 1) When I run left-right hemisphere paired t-test, can I add age as covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table? use this one-group, one-covariate example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> 2) I want to reorganize the hemisphere from left-right to symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it? Yes, though it is a little tricky with multiple ways, each complicated in its own way. 1. Create your own design matrix. You can use the one created by mri_glmfit to start. Assuming you want symptomHemi-nosymptomHemi, then, in each subject whose symptomHemi is rh, multiply its line in the design matrix by -1. Then pass this design matrix to mri_glmfit with --X instead of passing an FSGD file. 2. Load the output of mris_preproc into matlab, eg, y = MRIread('y.mgh');, then change the sign as in #1 above, eg, y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable subject. Then save the data with MRIwrite(y,'new.y.mgh');, then run mri_glmfit as normal with the new file. 3. Run mris_preproc for each subject separately to generate an lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the sign as in #1 above with fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o lh.lh-rh.thickness.sm00.subject10.mgh Then run mri_concat to concatenate all the subjects together in the same order as they are listed in the FSGD file, then use this stack as input the mri_glmfit Thanks for your patient and help. All best, Lanbo Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I try to use this code to compare left and right hemisphere by paired t-test and add age as covariate.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
which method are you trying to implement? If #3, then you need to run mris_preproc separately for each subject, and then run that fscalc command
On 11/07/2017 11:33 AM, lanbo Wang wrote:
Hi Douglas,
Thanks for your reply. I created the fsgd file as you show me, and run code like this. Am I right?
mris_preproc --fsgd Subject.xhemi.dat \ --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.age.sm00.mgh \ --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s subj_12_1 --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s subj_22_1 --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s subj_29_1 --s subj_32_1
mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir glm.lh.lh-rh.thickness.age.sm10 \ --fsgd Subject.xhemi.dat \ --C Avg-thickness-age-Cor.mtx \ --surf fsaverage_sym lh
Attachment is fsgd and Avg-thickness-age-cor.mtx.
All best, Lanbo Wang
On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Danny you need to give us more information if you want us to help you. Please include the command you ran and the entire screen output. cheers Bruce On Tue, 7 Nov 2017, Danny Deng wrote: Dear FDs, I encountered an odd situation: My free surfer will always shut down when I run command. My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel Core i5 I don’t know if the compatibility is fine with my download version (MacOS Lion OS X 10.7 (64b intel)Stable v6.0.0) Please kindly suggest. Thanks ver much Best Regards,Danny Deng On Nov 7, 2017, at 7:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: On 11/06/2017 12:03 PM, lanbo Wang wrote: Dear experts, I have two questions about hemisphere analysis: 1) When I run left-right hemisphere paired t-test, can I add age as covariate? If use fsgd to add covariate, to this paired t-test analysis, how to make the fsgd table? use this one-group, one-covariate example https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> 2) I want to reorganize the hemisphere from left-right to symptom-nosymptom according to body symptom side record and compare different between symptom hemisphere and nosymptom hemisphere. Can I use freesurfer to do it? Yes, though it is a little tricky with multiple ways, each complicated in its own way. 1. Create your own design matrix. You can use the one created by mri_glmfit to start. Assuming you want symptomHemi-nosymptomHemi, then, in each subject whose symptomHemi is rh, multiply its line in the design matrix by -1. Then pass this design matrix to mri_glmfit with --X instead of passing an FSGD file. 2. Load the output of mris_preproc into matlab, eg, y = MRIread('y.mgh');, then change the sign as in #1 above, eg, y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable subject. Then save the data with MRIwrite(y,'new.y.mgh');, then run mri_glmfit as normal with the new file. 3. Run mris_preproc for each subject separately to generate an lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the sign as in #1 above with fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o lh.lh-rh.thickness.sm00.subject10.mgh Then run mri_concat to concatenate all the subjects together in the same order as they are listed in the FSGD file, then use this stack as input the mri_glmfit Thanks for your patient and help. All best, Lanbo Wang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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which code. I gave 3 options below, which one did you use?
On 11/07/2017 02:43 PM, lanbo Wang wrote:
I try to use this code to compare left and right hemisphere by paired t-test and add age as covariate.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
which method are you trying to implement? If #3, then you need to run mris_preproc separately for each subject, and then run that fscalc command On 11/07/2017 11:33 AM, lanbo Wang wrote: > Hi Douglas, > > Thanks for your reply. > I created the fsgd file as you show me, and run code like this. Am I > right? > 1. > mris_preproc --fsgd Subject.xhemi.dat \ > --target fsaverage_sym --hemi lh \ > --xhemi --paired-diff \ > --srcsurfreg fsaverage_sym.sphere.reg \ > --meas thickness \ > --out lh.lh-rh.thickness.age.sm00.mgh \ > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s > subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s subj_12_1 > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s > subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s subj_22_1 > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s > subj_29_1 --s subj_32_1 > > 2. > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir > glm.lh.lh-rh.thickness.age.sm10 \ > --fsgd Subject.xhemi.dat \ > --C Avg-thickness-age-Cor.mtx \ > --surf fsaverage_sym lh > > Attachment is fsgd and Avg-thickness-age-cor.mtx. > > All best, > Lanbo Wang > > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi Danny > > you need to give us more information if you want us to help you. > Please include the command you ran and the entire screen output. > > cheers > Bruce > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > Dear FDs, > I encountered an odd situation: > > My free surfer will always shut down when I run command. > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel > Core i5 > > I don’t know if the compatibility is fine with my download > version (MacOS Lion OS X 10.7 (64b > intel)Stable v6.0.0) > > Please kindly suggest. > > Thanks ver much > > Best Regards,Danny Deng > > > On Nov 7, 2017, at 7:14 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > wrote: > > > > On 11/06/2017 12:03 PM, lanbo Wang wrote: > Dear experts, > > I have two questions about hemisphere analysis: > > 1) When I run left-right hemisphere paired t-test, can I > add age as > covariate? If use fsgd to add covariate, to this paired > t-test > analysis, how to make the fsgd table? > > use this one-group, one-covariate example > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>> > 2) I want to reorganize the hemisphere from left-right to > symptom-nosymptom according to body symptom side record > and compare > different between symptom hemisphere and nosymptom > hemisphere. Can I > use freesurfer to do it? > > Yes, though it is a little tricky with multiple ways, each > complicated > in its own way. > 1. Create your own design matrix. You can use the one created by > mri_glmfit to start. Assuming you want > symptomHemi-nosymptomHemi, then, > in each subject whose symptomHemi is rh, multiply its line in > the design > matrix by -1. Then pass this design matrix to mri_glmfit with --X > instead of passing an FSGD file. > 2. Load the output of mris_preproc into matlab, eg, y = > MRIread('y.mgh');, then change the sign as in #1 above, eg, > y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable > subject. Then save the data with MRIwrite(y,'new.y.mgh');, > then run > mri_glmfit as normal with the new file. > 3. Run mris_preproc for each subject separately to generate an > lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the > sign as in > #1 above with > fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o > lh.lh-rh.thickness.sm00.subject10.mgh > Then run mri_concat to concatenate all the subjects together > in the same > order as they are listed in the FSGD file, then use this stack > as input > the mri_glmfit > > > Thanks for your patient and help. > > All best, > Lanbo Wang > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > 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 Partners > Compliance HelpLine at > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . If the e-mail was > sent to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > 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 Partners > Compliance HelpLine at > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Dr. Douglas,
I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh sysname Linux hostname localhost.localdomain machine x86_64 user mtobia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh logyflag 0 usedti 0 labelmask /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label maskinv 0 glmdir glm.lh.lh-rh.thickness.sm10 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory glm.lh.lh-rh.thickness.sm10 Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 146902 points in label. Pruning voxels by thr: 0.000000 Found 146902 voxels in mask Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh Reshaping mriglm->mask... search space = 79288.081914 DOF = 0 ERROR: DOF = 0
The code I used before this one is How can I resolve this problem.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
which code. I gave 3 options below, which one did you use?
On 11/07/2017 02:43 PM, lanbo Wang wrote:
I try to use this code to compare left and right hemisphere by paired t-test and add age as covariate.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
which method are you trying to implement? If #3, then you need to run mris_preproc separately for each subject, and then run that fscalc command On 11/07/2017 11:33 AM, lanbo Wang wrote: > Hi Douglas, > > Thanks for your reply. > I created the fsgd file as you show me, and run code like this. AmI
> right? > 1. > mris_preproc --fsgd Subject.xhemi.dat \ > --target fsaverage_sym --hemi lh \ > --xhemi --paired-diff \ > --srcsurfreg fsaverage_sym.sphere.reg \ > --meas thickness \ > --out lh.lh-rh.thickness.age.sm00.mgh \ > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s > subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s subj_12_1 > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s > subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s subj_22_1 > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s > subj_29_1 --s subj_32_1 > > 2. > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir > glm.lh.lh-rh.thickness.age.sm10 \ > --fsgd Subject.xhemi.dat \ > --C Avg-thickness-age-Cor.mtx \ > --surf fsaverage_sym lh > > Attachment is fsgd and Avg-thickness-age-cor.mtx. > > All best, > Lanbo Wang > > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi Danny > > you need to give us more information if you want us to helpyou.
> Please include the command you ran and the entire screenoutput.
> > cheers > Bruce > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > Dear FDs, > I encountered an odd situation: > > My free surfer will always shut down when I run command. > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHzIntel
> Core i5 > > I don’t know if the compatibility is fine with my download > version (MacOS Lion OS X 10.7 (64b > intel)Stable v6.0.0) > > Please kindly suggest. > > Thanks ver much > > Best Regards,Danny Deng > > > On Nov 7, 2017, at 7:14 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> wrote: > > > > On 11/06/2017 12:03 PM, lanbo Wang wrote: > Dear experts, > > I have two questions about hemisphere analysis: > > 1) When I run left-right hemisphere paired t-test, can I > add age as > covariate? If use fsgd to add covariate, to this paired > t-test > analysis, how to make the fsgd table? > > use this one-group, one-covariate example > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>> > 2) I want to reorganize the hemisphere from left-right to > symptom-nosymptom according to body symptom side record > and compare > different between symptom hemisphere and nosymptom > hemisphere. Can I > use freesurfer to do it? > > Yes, though it is a little tricky with multiple ways, each > complicated > in its own way. > 1. Create your own design matrix. You can use the one created by > mri_glmfit to start. Assuming you want > symptomHemi-nosymptomHemi, then, > in each subject whose symptomHemi is rh, multiply its line in > the design > matrix by -1. Then pass this design matrix to mri_glmfit with --X > instead of passing an FSGD file. > 2. Load the output of mris_preproc into matlab, eg, y = > MRIread('y.mgh');, then change the sign as in #1 above, eg, > y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable > subject. Then save the data with MRIwrite(y,'new.y.mgh');, > then run > mri_glmfit as normal with the new file. > 3. Run mris_preproc for each subject separately to generate an > lh.lh-rh.thickness.sm00.subject10.mgh file. Then changethe
> sign as in > #1 above with > fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o > lh.lh-rh.thickness.sm00.subject10.mgh > Then run mri_concat to concatenate all the subjectstogether
> in the same > order as they are listed in the FSGD file, then use this stack > as input > the mri_glmfit > > > Thanks for your patient and help. > > All best, > Lanbo Wang > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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> sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > 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 Partners > Compliance HelpLine at > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Do you only have one subject in your input file? You need to run mris_preproc separately for each subject, create a different file for each, then mri_concat the files together
On 11/9/17 6:20 PM, lanbo Wang wrote:
Dr. Douglas,
I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh sysname Linux hostname localhost.localdomain machine x86_64 user mtobia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh logyflag 0 usedti 0 labelmask /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label maskinv 0 glmdir glm.lh.lh-rh.thickness.sm10 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory glm.lh.lh-rh.thickness.sm10 Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 146902 points in label. Pruning voxels by thr: 0.000000 Found 146902 voxels in mask Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh Reshaping mriglm->mask... search space = 79288.081914 DOF = 0 ERROR: DOF = 0
The code I used before this one is How can I resolve this problem.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
which code. I gave 3 options below, which one did you use? On 11/07/2017 02:43 PM, lanbo Wang wrote: > I try to use this code to compare left and right hemisphere by paired > t-test and add age as covariate. > > Thanks, > Lanbo > > On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > which method are you trying to implement? If #3, then you need to run > mris_preproc separately for each subject, and then run that fscalc > command > > > On 11/07/2017 11:33 AM, lanbo Wang wrote: > > Hi Douglas, > > > > Thanks for your reply. > > I created the fsgd file as you show me, and run code like this. Am I > > right? > > 1. > > mris_preproc --fsgd Subject.xhemi.dat \ > > --target fsaverage_sym --hemi lh \ > > --xhemi --paired-diff \ > > --srcsurfreg fsaverage_sym.sphere.reg \ > > --meas thickness \ > > --out lh.lh-rh.thickness.age.sm00.mgh \ > > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s > > subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s > subj_12_1 > > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s > > subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s > subj_22_1 > > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s > > subj_29_1 --s subj_32_1 > > > > 2. > > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir > > glm.lh.lh-rh.thickness.age.sm10 \ > > --fsgd Subject.xhemi.dat \ > > --C Avg-thickness-age-Cor.mtx \ > > --surf fsaverage_sym lh > > > > Attachment is fsgd and Avg-thickness-age-cor.mtx. > > > > All best, > > Lanbo Wang > > > > > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: > > > > Hi Danny > > > > you need to give us more information if you want us to help you. > > Please include the command you ran and the entire screen output. > > > > cheers > > Bruce > > > > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > > > Dear FDs, > > I encountered an odd situation: > > > > My free surfer will always shut down when I run command. > > > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel > > Core i5 > > > > I don’t know if the compatibility is fine with my download > > version (MacOS Lion OS X 10.7 (64b > > intel)Stable v6.0.0) > > > > Please kindly suggest. > > > > Thanks ver much > > > > Best Regards,Danny Deng > > > > > > On Nov 7, 2017, at 7:14 AM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > wrote: > > > > > > > > On 11/06/2017 12:03 PM, lanbo Wang wrote: > > Dear experts, > > > > I have two questions about hemisphere analysis: > > > > 1) When I run left-right hemisphere paired t-test, > can I > > add age as > > covariate? If use fsgd to add covariate, to this > paired > > t-test > > analysis, how to make the fsgd table? > > > > use this one-group, one-covariate example > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>>> > > 2) I want to reorganize the hemisphere from > left-right to > > symptom-nosymptom according to body symptom side > record > > and compare > > different between symptom hemisphere and nosymptom > > hemisphere. Can I > > use freesurfer to do it? > > > > Yes, though it is a little tricky with multiple ways, each > > complicated > > in its own way. > > 1. Create your own design matrix. You can use the one > created by > > mri_glmfit to start. Assuming you want > > symptomHemi-nosymptomHemi, then, > > in each subject whose symptomHemi is rh, multiply its > line in > > the design > > matrix by -1. Then pass this design matrix to mri_glmfit > with --X > > instead of passing an FSGD file. > > 2. Load the output of mris_preproc into matlab, eg, y = > > MRIread('y.mgh');, then change the sign as in #1 above, eg, > > y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each > applicable > > subject. Then save the data with MRIwrite(y,'new.y.mgh');, > > then run > > mri_glmfit as normal with the new file. > > 3. Run mris_preproc for each subject separately to > generate an > > lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the > > sign as in > > #1 above with > > fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o > > lh.lh-rh.thickness.sm00.subject10.mgh > > Then run mri_concat to concatenate all the subjects together > > in the same > > order as they are listed in the FSGD file, then use this > stack > > as input > > the mri_glmfit > > > > > > Thanks for your patient and help. > > > > All best, > > Lanbo Wang > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > -- > > Douglas N. 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If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. 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I firstly did mris_preproc separately. Secondly used fscalc to reverse left symptom subjects. Thirdly used mri_concat --conjunct to combine all the subjects together.
The code is: 1.mris_preproc --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.s02.mgh \ --s subj_02_1 2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o lh.lh-rh.thickness.sm00.s09.mgh 3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh 4.smooth 5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Do you only have one subject in your input file? You need to run mris_preproc separately for each subject, create a different file for each, then mri_concat the files together
On 11/9/17 6:20 PM, lanbo Wang wrote:
Dr. Douglas,
I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom/ /fsaverage_sym/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh sysname Linux hostname localhost.localdomain machine x86_64 user mtobia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh. thickness.sm10.mgh logyflag 0 usedti 0 labelmask /HD4/subjects_results_symptom//fsaverage_sym/label/lh. cortex.label maskinv 0 glmdir glm.lh.lh-rh.thickness.sm10 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory glm.lh.lh-rh.thickness.sm10 Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh. thickness.sm10.mgh Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 146902 points in label. Pruning voxels by thr: 0.000000 Found 146902 voxels in mask Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh Reshaping mriglm->mask... search space = 79288.081914 DOF = 0 ERROR: DOF = 0
The code I used before this one is How can I resolve this problem.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
which code. I gave 3 options below, which one did you use?
On 11/07/2017 02:43 PM, lanbo Wang wrote:
I try to use this code to compare left and right hemisphere by paired t-test and add age as covariate.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
which method are you trying to implement? If #3, then you need torun
mris_preproc separately for each subject, and then run that fscalc command On 11/07/2017 11:33 AM, lanbo Wang wrote: > Hi Douglas, > > Thanks for your reply. > I created the fsgd file as you show me, and run code like this.Am I
> right? > 1. > mris_preproc --fsgd Subject.xhemi.dat \ > --target fsaverage_sym --hemi lh \ > --xhemi --paired-diff \ > --srcsurfreg fsaverage_sym.sphere.reg \ > --meas thickness \ > --out lh.lh-rh.thickness.age.sm00.mgh \ > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s > subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s subj_12_1 > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s > subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s subj_22_1 > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s > subj_29_1 --s subj_32_1 > > 2. > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir > glm.lh.lh-rh.thickness.age.sm10 \ > --fsgd Subject.xhemi.dat \ > --C Avg-thickness-age-Cor.mtx \ > --surf fsaverage_sym lh > > Attachment is fsgd and Avg-thickness-age-cor.mtx. > > All best, > Lanbo Wang > > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi Danny > > you need to give us more information if you want us to helpyou.
> Please include the command you ran and the entire screenoutput.
> > cheers > Bruce > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > Dear FDs, > I encountered an odd situation: > > My free surfer will always shut down when I run command. > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHzIntel
> Core i5 > > I don’t know if the compatibility is fine with my download > version (MacOS Lion OS X 10.7 (64b > intel)Stable v6.0.0) > > Please kindly suggest. > > Thanks ver much > > Best Regards,Danny Deng > > > On Nov 7, 2017, at 7:14 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> wrote: > > > > On 11/06/2017 12:03 PM, lanbo Wang wrote: > Dear experts, > > I have two questions about hemisphere analysis: > > 1) When I run left-right hemisphere paired t-test, can I > add age as > covariate? If use fsgd to add covariate, to this paired > t-test > analysis, how to make the fsgd table? > > use this one-group, one-covariate example > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>> > 2) I want to reorganize the hemisphere from left-right to > symptom-nosymptom according to body symptom side record > and compare > different between symptom hemisphere and nosymptom > hemisphere. Can I > use freesurfer to do it? > > Yes, though it is a little tricky with multiple ways, each > complicated > in its own way. > 1. Create your own design matrix. You can use the one created by > mri_glmfit to start. Assuming you want > symptomHemi-nosymptomHemi, then, > in each subject whose symptomHemi is rh, multiply its line in > the design > matrix by -1. Then pass this design matrix to mri_glmfit with --X > instead of passing an FSGD file. > 2. Load the output of mris_preproc into matlab, eg, y = > MRIread('y.mgh');, then change the sign as in #1 above,eg,
> y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable > subject. Then save the data with MRIwrite(y,'new.y.mgh');, > then run > mri_glmfit as normal with the new file. > 3. Run mris_preproc for each subject separately to generate an > lh.lh-rh.thickness.sm00.subject10.mgh file. Then changethe
> sign as in > #1 above with > fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o > lh.lh-rh.thickness.sm00.subject10.mgh > Then run mri_concat to concatenate all the subjectstogether
> in the same > order as they are listed in the FSGD file, then use this stack > as input > the mri_glmfit > > > Thanks for your patient and help. > > All best, > Lanbo Wang > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Don't use --conjunct, just mri_concat file1 file2 ... file N --o output
On 11/10/17 12:56 PM, lanbo Wang wrote:
I firstly did mris_preproc separately. Secondly used fscalc to reverse left symptom subjects. Thirdly used mri_concat --conjunct to combine all the subjects together.
The code is: 1.mris_preproc --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.s02.mgh \ --s subj_02_1 2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o lh.lh-rh.thickness.sm00.s09.mgh 3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh 4.smooth 5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Do you only have one subject in your input file? You need to run mris_preproc separately for each subject, create a different file for each, then mri_concat the files together On 11/9/17 6:20 PM, lanbo Wang wrote:Dr. Douglas, I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh sysname Linux hostname localhost.localdomain machine x86_64 user mtobia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh logyflag 0 usedti 0 labelmask /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label maskinv 0 glmdir glm.lh.lh-rh.thickness.sm10 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory glm.lh.lh-rh.thickness.sm10 Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 146902 points in label. Pruning voxels by thr: 0.000000 Found 146902 voxels in mask Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh Reshaping mriglm->mask... search space = 79288.081914 DOF = 0 ERROR: DOF = 0 The code I used before this one is How can I resolve this problem. Thanks, Lanbo On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: which code. I gave 3 options below, which one did you use? On 11/07/2017 02:43 PM, lanbo Wang wrote: > I try to use this code to compare left and right hemisphere by paired > t-test and add age as covariate. > > Thanks, > Lanbo > > On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > which method are you trying to implement? If #3, then you need to run > mris_preproc separately for each subject, and then run that fscalc > command > > > On 11/07/2017 11:33 AM, lanbo Wang wrote: > > Hi Douglas, > > > > Thanks for your reply. > > I created the fsgd file as you show me, and run code like this. Am I > > right? > > 1. > > mris_preproc --fsgd Subject.xhemi.dat \ > > --target fsaverage_sym --hemi lh \ > > --xhemi --paired-diff \ > > --srcsurfreg fsaverage_sym.sphere.reg \ > > --meas thickness \ > > --out lh.lh-rh.thickness.age.sm00.mg <http://lh.lh-rh.thickness.age.sm00.mg>h \ > > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s > > subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s > subj_12_1 > > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s > > subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s > subj_22_1 > > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s > > subj_29_1 --s subj_32_1 > > > > 2. > > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mg <http://lh.lh-rh.thickness.age.sm10.mg>h --glmdir > > glm.lh.lh-rh.thickness.age.sm10 \ > > --fsgd Subject.xhemi.dat \ > > --C Avg-thickness-age-Cor.mtx \ > > --surf fsaverage_sym lh > > > > Attachment is fsgd and Avg-thickness-age-cor.mtx. > > > > All best, > > Lanbo Wang > > > > > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: > > > > Hi Danny > > > > you need to give us more information if you want us to help you. > > Please include the command you ran and the entire screen output. > > > > cheers > > Bruce > > > > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > > > Dear FDs, > > I encountered an odd situation: > > > > My free surfer will always shut down when I run command. > > > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel > > Core i5 > > > > I don’t know if the compatibility is fine with my download > > version (MacOS Lion OS X 10.7 (64b > > intel)Stable v6.0.0) > > > > Please kindly suggest. > > > > Thanks ver much > > > > Best Regards,Danny Deng > > > > > > On Nov 7, 2017, at 7:14 AM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > wrote: > > > > > > > > On 11/06/2017 12:03 PM, lanbo Wang wrote: > > Dear experts, > > > > I have two questions about hemisphere analysis: > > > > 1) When I run left-right hemisphere paired t-test, > can I > > add age as > > covariate? If use fsgd to add covariate, to this > paired > > t-test > > analysis, how to make the fsgd table? > > > > use this one-group, one-covariate example > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>>> > > 2) I want to reorganize the hemisphere from > left-right to > > symptom-nosymptom according to body symptom side > record > > and compare > > different between symptom hemisphere and nosymptom > > hemisphere. Can I > > use freesurfer to do it? > > > > Yes, though it is a little tricky with multiple ways, each > > complicated > > in its own way. > > 1. Create your own design matrix. You can use the one > created by > > mri_glmfit to start. Assuming you want > > symptomHemi-nosymptomHemi, then, > > in each subject whose symptomHemi is rh, multiply its > line in > > the design > > matrix by -1. Then pass this design matrix to mri_glmfit > with --X > > instead of passing an FSGD file. > > 2. Load the output of mris_preproc into matlab, eg, y = > > MRIread('y.mgh');, then change the sign as in #1 above, eg, > > y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each > applicable > > subject. Then save the data with MRIwrite(y,'new.y.mgh');, > > then run > > mri_glmfit as normal with the new file. > > 3. Run mris_preproc for each subject separately to > generate an > > lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the > > sign as in > > #1 above with > > fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o > > lh.lh-rh.thickness.sm00.subject10.mgh > > Then run mri_concat to concatenate all the subjects together > > in the same > > order as they are listed in the FSGD file, then use this > stack > > as input > > the mri_glmfit > > > > > > Thanks for your patient and help. > > > > All best, > > Lanbo Wang > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > -- > > Douglas N. 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If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. 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Thank you very much, it's work. I have another question, this is for structural imaging. Can I use those steps for fmri or DTI imaging?
On Fri, Nov 10, 2017 at 1:08 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Don't use --conjunct, just mri_concat file1 file2 ... file N --o output
On 11/10/17 12:56 PM, lanbo Wang wrote:
I firstly did mris_preproc separately. Secondly used fscalc to reverse left symptom subjects. Thirdly used mri_concat --conjunct to combine all the subjects together.
The code is: 1.mris_preproc --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.s02.mgh \ --s subj_02_1 2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o lh.lh-rh.thickness.sm00.s09.mgh 3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh 4.smooth 5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Do you only have one subject in your input file? You need to run mris_preproc separately for each subject, create a different file for each, then mri_concat the files together
On 11/9/17 6:20 PM, lanbo Wang wrote:
Dr. Douglas,
I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom/ /fsaverage_sym/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh sysname Linux hostname localhost.localdomain machine x86_64 user mtobia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th ickness.sm10.mgh logyflag 0 usedti 0 labelmask /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex .label maskinv 0 glmdir glm.lh.lh-rh.thickness.sm10 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory glm.lh.lh-rh.thickness.sm10 Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/ lh.lh-rh.thickness.sm10.mgh Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 146902 points in label. Pruning voxels by thr: 0.000000 Found 146902 voxels in mask Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh Reshaping mriglm->mask... search space = 79288.081914 DOF = 0 ERROR: DOF = 0
The code I used before this one is How can I resolve this problem.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
which code. I gave 3 options below, which one did you use?
On 11/07/2017 02:43 PM, lanbo Wang wrote:
I try to use this code to compare left and right hemisphere by paired t-test and add age as covariate.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
which method are you trying to implement? If #3, then you need torun
mris_preproc separately for each subject, and then run that fscalc command On 11/07/2017 11:33 AM, lanbo Wang wrote: > Hi Douglas, > > Thanks for your reply. > I created the fsgd file as you show me, and run code like this.Am I
> right? > 1. > mris_preproc --fsgd Subject.xhemi.dat \ > --target fsaverage_sym --hemi lh \ > --xhemi --paired-diff \ > --srcsurfreg fsaverage_sym.sphere.reg \ > --meas thickness \ > --out lh.lh-rh.thickness.age.sm00.mgh \ > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s > subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s subj_12_1 > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s > subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s subj_22_1 > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s > subj_29_1 --s subj_32_1 > > 2. > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir > glm.lh.lh-rh.thickness.age.sm10 \ > --fsgd Subject.xhemi.dat \ > --C Avg-thickness-age-Cor.mtx \ > --surf fsaverage_sym lh > > Attachment is fsgd and Avg-thickness-age-cor.mtx. > > All best, > Lanbo Wang > > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi Danny > > you need to give us more information if you want us to helpyou.
> Please include the command you ran and the entire screenoutput.
> > cheers > Bruce > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > Dear FDs, > I encountered an odd situation: > > My free surfer will always shut down when I run command. > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHzIntel
> Core i5 > > I don’t know if the compatibility is fine with mydownload
> version (MacOS Lion OS X 10.7 (64b > intel)Stable v6.0.0) > > Please kindly suggest. > > Thanks ver much > > Best Regards,Danny Deng > > > On Nov 7, 2017, at 7:14 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> wrote: > > > > On 11/06/2017 12:03 PM, lanbo Wang wrote: > Dear experts, > > I have two questions about hemisphere analysis: > > 1) When I run left-right hemisphere paired t-test, can I > add age as > covariate? If use fsgd to add covariate, to this paired > t-test > analysis, how to make the fsgd table? > > use this one-group, one-covariate example > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>> > 2) I want to reorganize the hemisphere from left-right to > symptom-nosymptom according to body symptom side record > and compare > different between symptom hemisphere and nosymptom > hemisphere. Can I > use freesurfer to do it? > > Yes, though it is a little tricky with multiple ways,each
> complicated > in its own way. > 1. Create your own design matrix. You can use the one created by > mri_glmfit to start. Assuming you want > symptomHemi-nosymptomHemi, then, > in each subject whose symptomHemi is rh, multiply its line in > the design > matrix by -1. Then pass this design matrix to mri_glmfit with --X > instead of passing an FSGD file. > 2. Load the output of mris_preproc into matlab, eg, y = > MRIread('y.mgh');, then change the sign as in #1 above,eg,
> y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable > subject. Then save the data withMRIwrite(y,'new.y.mgh');,
> then run > mri_glmfit as normal with the new file. > 3. Run mris_preproc for each subject separately to generate an > lh.lh-rh.thickness.sm00.subject10.mgh file. Then changethe
> sign as in > #1 above with > fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o > lh.lh-rh.thickness.sm00.subject10.mgh > Then run mri_concat to concatenate all the subjectstogether
> in the same > order as they are listed in the FSGD file, then use this stack > as input > the mri_glmfit > > > Thanks for your patient and help. > > All best, > Lanbo Wang > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Yes
On 11/10/17 2:45 PM, lanbo Wang wrote:
Thank you very much, it's work. I have another question, this is for structural imaging. Can I use those steps for fmri or DTI imaging?
On Fri, Nov 10, 2017 at 1:08 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Don't use --conjunct, just mri_concat file1 file2 ... file N --o output On 11/10/17 12:56 PM, lanbo Wang wrote:I firstly did mris_preproc separately. Secondly used fscalc to reverse left symptom subjects. Thirdly used mri_concat --conjunct to combine all the subjects together. The code is: 1.mris_preproc --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.s02.mgh \ --s subj_02_1 2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o lh.lh-rh.thickness.sm00.s09.mgh 3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh 4.smooth 5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Do you only have one subject in your input file? You need to run mris_preproc separately for each subject, create a different file for each, then mri_concat the files together On 11/9/17 6:20 PM, lanbo Wang wrote:Dr. Douglas, I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh sysname Linux hostname localhost.localdomain machine x86_64 user mtobia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th <http://lh.lh-rh.th>ickness.sm10.mgh logyflag 0 usedti 0 labelmask /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label maskinv 0 glmdir glm.lh.lh-rh.thickness.sm10 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory glm.lh.lh-rh.thickness.sm10 Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th <http://lh.lh-rh.th>ickness.sm10.mgh Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 146902 points in label. Pruning voxels by thr: 0.000000 Found 146902 voxels in mask Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh Reshaping mriglm->mask... search space = 79288.081914 DOF = 0 ERROR: DOF = 0 The code I used before this one is How can I resolve this problem. Thanks, Lanbo On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: which code. I gave 3 options below, which one did you use? On 11/07/2017 02:43 PM, lanbo Wang wrote: > I try to use this code to compare left and right hemisphere by paired > t-test and add age as covariate. > > Thanks, > Lanbo > > On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > which method are you trying to implement? If #3, then you need to run > mris_preproc separately for each subject, and then run that fscalc > command > > > On 11/07/2017 11:33 AM, lanbo Wang wrote: > > Hi Douglas, > > > > Thanks for your reply. > > I created the fsgd file as you show me, and run code like this. Am I > > right? > > 1. > > mris_preproc --fsgd Subject.xhemi.dat \ > > --target fsaverage_sym --hemi lh \ > > --xhemi --paired-diff \ > > --srcsurfreg fsaverage_sym.sphere.reg \ > > --meas thickness \ > > --out lh.lh-rh.thickness.age.sm00.mg <http://lh.lh-rh.thickness.age.sm00.mg>h \ > > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s > > subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s > subj_12_1 > > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s > > subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s > subj_22_1 > > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s > > subj_29_1 --s subj_32_1 > > > > 2. > > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mg <http://lh.lh-rh.thickness.age.sm10.mg>h --glmdir > > glm.lh.lh-rh.thickness.age.sm10 \ > > --fsgd Subject.xhemi.dat \ > > --C Avg-thickness-age-Cor.mtx \ > > --surf fsaverage_sym lh > > > > Attachment is fsgd and Avg-thickness-age-cor.mtx. > > > > All best, > > Lanbo Wang > > > > > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: > > > > Hi Danny > > > > you need to give us more information if you want us to help you. > > Please include the command you ran and the entire screen output. > > > > cheers > > Bruce > > > > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > > > Dear FDs, > > I encountered an odd situation: > > > > My free surfer will always shut down when I run command. > > > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel > > Core i5 > > > > I don’t know if the compatibility is fine with my download > > version (MacOS Lion OS X 10.7 (64b > > intel)Stable v6.0.0) > > > > Please kindly suggest. > > > > Thanks ver much > > > > Best Regards,Danny Deng > > > > > > On Nov 7, 2017, at 7:14 AM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > wrote: > > > > > > > > On 11/06/2017 12:03 PM, lanbo Wang wrote: > > Dear experts, > > > > I have two questions about hemisphere analysis: > > > > 1) When I run left-right hemisphere paired t-test, > can I > > add age as > > covariate? If use fsgd to add covariate, to this > paired > > t-test > > analysis, how to make the fsgd table? > > > > use this one-group, one-covariate example > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>>> > > 2) I want to reorganize the hemisphere from > left-right to > > symptom-nosymptom according to body symptom side > record > > and compare > > different between symptom hemisphere and nosymptom > > hemisphere. Can I > > use freesurfer to do it? > > > > Yes, though it is a little tricky with multiple ways, each > > complicated > > in its own way. > > 1. Create your own design matrix. You can use the one > created by > > mri_glmfit to start. Assuming you want > > symptomHemi-nosymptomHemi, then, > > in each subject whose symptomHemi is rh, multiply its > line in > > the design > > matrix by -1. Then pass this design matrix to mri_glmfit > with --X > > instead of passing an FSGD file. > > 2. Load the output of mris_preproc into matlab, eg, y = > > MRIread('y.mgh');, then change the sign as in #1 above, eg, > > y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each > applicable > > subject. Then save the data with MRIwrite(y,'new.y.mgh');, > > then run > > mri_glmfit as normal with the new file. > > 3. Run mris_preproc for each subject separately to > generate an > > lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the > > sign as in > > #1 above with > > fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o > > lh.lh-rh.thickness.sm00.subject10.mgh > > Then run mri_concat to concatenate all the subjects together > > in the same > > order as they are listed in the FSGD file, then use this > stack > > as input > > the mri_glmfit > > > > > > Thanks for your patient and help. > > > > All best, > > Lanbo Wang > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > 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 Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> . If the e-mail was > > sent to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > 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 Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> . If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. 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Can I use data processed by other tool like FSL, or I can only use DTI image after Freesurfer processing?
On Fri, Nov 10, 2017 at 3:07 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Yes
On 11/10/17 2:45 PM, lanbo Wang wrote:
Thank you very much, it's work. I have another question, this is for structural imaging. Can I use those steps for fmri or DTI imaging?
On Fri, Nov 10, 2017 at 1:08 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Don't use --conjunct, just mri_concat file1 file2 ... file N --o output
On 11/10/17 12:56 PM, lanbo Wang wrote:
I firstly did mris_preproc separately. Secondly used fscalc to reverse left symptom subjects. Thirdly used mri_concat --conjunct to combine all the subjects together.
The code is: 1.mris_preproc --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.s02.mgh \ --s subj_02_1 2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o lh.lh-rh.thickness.sm00.s09.mgh 3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh 4.smooth 5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote:
Do you only have one subject in your input file? You need to run mris_preproc separately for each subject, create a different file for each, then mri_concat the files together
On 11/9/17 6:20 PM, lanbo Wang wrote:
Dr. Douglas,
I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom/ /fsaverage_sym/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh sysname Linux hostname localhost.localdomain machine x86_64 user mtobia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th ickness.sm10.mgh logyflag 0 usedti 0 labelmask /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex .label maskinv 0 glmdir glm.lh.lh-rh.thickness.sm10 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory glm.lh.lh-rh.thickness.sm10 Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/ lh.lh-rh.thickness.sm10.mgh Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 146902 points in label. Pruning voxels by thr: 0.000000 Found 146902 voxels in mask Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh Reshaping mriglm->mask... search space = 79288.081914 DOF = 0 ERROR: DOF = 0
The code I used before this one is How can I resolve this problem.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
which code. I gave 3 options below, which one did you use?
On 11/07/2017 02:43 PM, lanbo Wang wrote:
I try to use this code to compare left and right hemisphere by paired t-test and add age as covariate.
Thanks, Lanbo
On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
which method are you trying to implement? If #3, then you need torun
mris_preproc separately for each subject, and then run that fscalc command On 11/07/2017 11:33 AM, lanbo Wang wrote: > Hi Douglas, > > Thanks for your reply. > I created the fsgd file as you show me, and run code like this.Am I
> right? > 1. > mris_preproc --fsgd Subject.xhemi.dat \ > --target fsaverage_sym --hemi lh \ > --xhemi --paired-diff \ > --srcsurfreg fsaverage_sym.sphere.reg \ > --meas thickness \ > --out lh.lh-rh.thickness.age.sm00.mgh \ > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s > subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s subj_12_1 > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s > subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s subj_22_1 > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s > subj_29_1 --s subj_32_1 > > 2. > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir > glm.lh.lh-rh.thickness.age.sm10 \ > --fsgd Subject.xhemi.dat \ > --C Avg-thickness-age-Cor.mtx \ > --surf fsaverage_sym lh > > Attachment is fsgd and Avg-thickness-age-cor.mtx. > > All best, > Lanbo Wang > > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi Danny > > you need to give us more information if you want us to helpyou.
> Please include the command you ran and the entire screenoutput.
> > cheers > Bruce > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > Dear FDs, > I encountered an odd situation: > > My free surfer will always shut down when I run command. > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHzIntel
> Core i5 > > I don’t know if the compatibility is fine with mydownload
> version (MacOS Lion OS X 10.7 (64b > intel)Stable v6.0.0) > > Please kindly suggest. > > Thanks ver much > > Best Regards,Danny Deng > > > On Nov 7, 2017, at 7:14 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> wrote: > > > > On 11/06/2017 12:03 PM, lanbo Wang wrote: > Dear experts, > > I have two questions about hemisphere analysis: > > 1) When I run left-right hemisphere paired t-test, can I > add age as > covariate? If use fsgd to add covariate, to this paired > t-test > analysis, how to make the fsgd table? > > use this one-group, one-covariate example > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>> > 2) I want to reorganize the hemisphere from left-right to > symptom-nosymptom according to body symptom side record > and compare > different between symptom hemisphere and nosymptom > hemisphere. Can I > use freesurfer to do it? > > Yes, though it is a little tricky with multiple ways,each
> complicated > in its own way. > 1. Create your own design matrix. You can use the one created by > mri_glmfit to start. Assuming you want > symptomHemi-nosymptomHemi, then, > in each subject whose symptomHemi is rh, multiply its line in > the design > matrix by -1. Then pass this design matrix to mri_glmfit with --X > instead of passing an FSGD file. > 2. Load the output of mris_preproc into matlab, eg, y = > MRIread('y.mgh');, then change the sign as in #1 above,eg,
> y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable > subject. Then save the data withMRIwrite(y,'new.y.mgh');,
> then run > mri_glmfit as normal with the new file. > 3. Run mris_preproc for each subject separately to generate an > lh.lh-rh.thickness.sm00.subject10.mgh file. Thenchange the
> sign as in > #1 above with > fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o > lh.lh-rh.thickness.sm00.subject10.mgh > Then run mri_concat to concatenate all the subjectstogether
> in the same > order as they are listed in the FSGD file, then use this stack > as input > the mri_glmfit > > > Thanks for your patient and help. > > All best, > Lanbo Wang > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
you can use anything that you can register the the FS anatomical
On 11/13/2017 04:34 PM, lanbo Wang wrote:
Can I use data processed by other tool like FSL, or I can only use DTI image after Freesurfer processing?
On Fri, Nov 10, 2017 at 3:07 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yes On 11/10/17 2:45 PM, lanbo Wang wrote:Thank you very much, it's work. I have another question, this is for structural imaging. Can I use those steps for fmri or DTI imaging? On Fri, Nov 10, 2017 at 1:08 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Don't use --conjunct, just mri_concat file1 file2 ... file N --o output On 11/10/17 12:56 PM, lanbo Wang wrote:I firstly did mris_preproc separately. Secondly used fscalc to reverse left symptom subjects. Thirdly used mri_concat --conjunct to combine all the subjects together. The code is: 1.mris_preproc --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.s02.mg <http://lh.lh-rh.thickness.sm00.s02.mg>h \ --s subj_02_1 2. fscalc lh.lh-rh.thickness.sm00.s09.mg <http://lh.lh-rh.thickness.sm00.s09.mg>h mul -1 -o lh.lh-rh.thickness.sm00.s09.mg <http://lh.lh-rh.thickness.sm00.s09.mg>h 3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mg <http://lh.lh-rh.thickness.sm00.s02.mg>h lh.lh-rh.thickness.sm00.s03.mg <http://lh.lh-rh.thickness.sm00.s03.mg>h lh.lh-rh.thickness.sm00.s04.mg <http://lh.lh-rh.thickness.sm00.s04.mg>h lh.lh-rh.thickness.sm00.s05.mg <http://lh.lh-rh.thickness.sm00.s05.mg>h lh.lh-rh.thickness.sm00.s06.mg <http://lh.lh-rh.thickness.sm00.s06.mg>h lh.lh-rh.thickness.sm00.s08.mg <http://lh.lh-rh.thickness.sm00.s08.mg>h lh.lh-rh.thickness.sm00.s09.mg <http://lh.lh-rh.thickness.sm00.s09.mg>h lh.lh-rh.thickness.sm00.s10.mg <http://lh.lh-rh.thickness.sm00.s10.mg>h lh.lh-rh.thickness.sm00.s11.mg <http://lh.lh-rh.thickness.sm00.s11.mg>h lh.lh-rh.thickness.sm00.s12.mg <http://lh.lh-rh.thickness.sm00.s12.mg>h lh.lh-rh.thickness.sm00.s13.mg <http://lh.lh-rh.thickness.sm00.s13.mg>h lh.lh-rh.thickness.sm00.s14.mg <http://lh.lh-rh.thickness.sm00.s14.mg>h lh.lh-rh.thickness.sm00.s15.mg <http://lh.lh-rh.thickness.sm00.s15.mg>h lh.lh-rh.thickness.sm00.s16.mg <http://lh.lh-rh.thickness.sm00.s16.mg>h lh.lh-rh.thickness.sm00.s17.mg <http://lh.lh-rh.thickness.sm00.s17.mg>h lh.lh-rh.thickness.sm00.s18.mg <http://lh.lh-rh.thickness.sm00.s18.mg>h lh.lh-rh.thickness.sm00.s19.mg <http://lh.lh-rh.thickness.sm00.s19.mg>h lh.lh-rh.thickness.sm00.s20.mg <http://lh.lh-rh.thickness.sm00.s20.mg>h lh.lh-rh.thickness.sm00.s21.mg <http://lh.lh-rh.thickness.sm00.s21.mg>h lh.lh-rh.thickness.sm00.s22.mg <http://lh.lh-rh.thickness.sm00.s22.mg>h lh.lh-rh.thickness.sm00.s24.mg <http://lh.lh-rh.thickness.sm00.s24.mg>h lh.lh-rh.thickness.sm00.s25.mg <http://lh.lh-rh.thickness.sm00.s25.mg>h lh.lh-rh.thickness.sm00.s26.mg <http://lh.lh-rh.thickness.sm00.s26.mg>h lh.lh-rh.thickness.sm00.s27.mg <http://lh.lh-rh.thickness.sm00.s27.mg>h lh.lh-rh.thickness.sm00.s29.mg <http://lh.lh-rh.thickness.sm00.s29.mg>h lh.lh-rh.thickness.sm00.s32.mg <http://lh.lh-rh.thickness.sm00.s32.mg>h --o lh.lh-rh.thickness.sm00.mgh 4.smooth 5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Do you only have one subject in your input file? You need to run mris_preproc separately for each subject, create a different file for each, then mri_concat the files together On 11/9/17 6:20 PM, lanbo Wang wrote:Dr. Douglas, I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh sysname Linux hostname localhost.localdomain machine x86_64 user mtobia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th <http://lh.lh-rh.th>ickness.sm10.mgh logyflag 0 usedti 0 labelmask /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label maskinv 0 glmdir glm.lh.lh-rh.thickness.sm10 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory glm.lh.lh-rh.thickness.sm10 Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th <http://lh.lh-rh.th>ickness.sm10.mgh Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 146902 points in label. Pruning voxels by thr: 0.000000 Found 146902 voxels in mask Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh Reshaping mriglm->mask... search space = 79288.081914 DOF = 0 ERROR: DOF = 0 The code I used before this one is How can I resolve this problem. Thanks, Lanbo On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: which code. I gave 3 options below, which one did you use? On 11/07/2017 02:43 PM, lanbo Wang wrote: > I try to use this code to compare left and right hemisphere by paired > t-test and add age as covariate. > > Thanks, > Lanbo > > On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > which method are you trying to implement? If #3, then you need to run > mris_preproc separately for each subject, and then run that fscalc > command > > > On 11/07/2017 11:33 AM, lanbo Wang wrote: > > Hi Douglas, > > > > Thanks for your reply. > > I created the fsgd file as you show me, and run code like this. Am I > > right? > > 1. > > mris_preproc --fsgd Subject.xhemi.dat \ > > --target fsaverage_sym --hemi lh \ > > --xhemi --paired-diff \ > > --srcsurfreg fsaverage_sym.sphere.reg \ > > --meas thickness \ > > --out lh.lh-rh.thickness.age.sm00.mg <http://lh.lh-rh.thickness.age.sm00.mg>h \ > > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s > > subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s > subj_12_1 > > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s > > subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s > subj_22_1 > > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s > > subj_29_1 --s subj_32_1 > > > > 2. > > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mg <http://lh.lh-rh.thickness.age.sm10.mg>h --glmdir > > glm.lh.lh-rh.thickness.age.sm10 \ > > --fsgd Subject.xhemi.dat \ > > --C Avg-thickness-age-Cor.mtx \ > > --surf fsaverage_sym lh > > > > Attachment is fsgd and Avg-thickness-age-cor.mtx. > > > > All best, > > Lanbo Wang > > > > > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: > > > > Hi Danny > > > > you need to give us more information if you want us to help you. > > Please include the command you ran and the entire screen output. > > > > cheers > > Bruce > > > > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > > > Dear FDs, > > I encountered an odd situation: > > > > My free surfer will always shut down when I run command. > > > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel > > Core i5 > > > > I don’t know if the compatibility is fine with my download > > version (MacOS Lion OS X 10.7 (64b > > intel)Stable v6.0.0) > > > > Please kindly suggest. > > > > Thanks ver much > > > > Best Regards,Danny Deng > > > > > > On Nov 7, 2017, at 7:14 AM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > wrote: > > > > > > > > On 11/06/2017 12:03 PM, lanbo Wang wrote: > > Dear experts, > > > > I have two questions about hemisphere analysis: > > > > 1) When I run left-right hemisphere paired t-test, > can I > > add age as > > covariate? If use fsgd to add covariate, to this > paired > > t-test > > analysis, how to make the fsgd table? > > > > use this one-group, one-covariate example > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>>> > > 2) I want to reorganize the hemisphere from > left-right to > > symptom-nosymptom according to body symptom side > record > > and compare > > different between symptom hemisphere and nosymptom > > hemisphere. Can I > > use freesurfer to do it? > > > > Yes, though it is a little tricky with multiple ways, each > > complicated > > in its own way. > > 1. Create your own design matrix. You can use the one > created by > > mri_glmfit to start. Assuming you want > > symptomHemi-nosymptomHemi, then, > > in each subject whose symptomHemi is rh, multiply its > line in > > the design > > matrix by -1. Then pass this design matrix to mri_glmfit > with --X > > instead of passing an FSGD file. > > 2. Load the output of mris_preproc into matlab, eg, y = > > MRIread('y.mgh');, then change the sign as in #1 above, eg, > > y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each > applicable > > subject. Then save the data with MRIwrite(y,'new.y.mgh');, > > then run > > mri_glmfit as normal with the new file. > > 3. Run mris_preproc for each subject separately to > generate an > > lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the > > sign as in > > #1 above with > > fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o > > lh.lh-rh.thickness.sm00.subject10.mgh > > Then run mri_concat to concatenate all the subjects together > > in the same > > order as they are listed in the FSGD file, then use this > stack > > as input > > the mri_glmfit > > > > > > Thanks for your patient and help. > > > > All best, > > Lanbo Wang > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > 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 Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> . If the e-mail was > > sent to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > > > > > 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 Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> . If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. 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Hi,
I want to compare structure changes rate between left and right using longitudinal data. I found when I use xhemi, but the changes rate file (rate, pc-1, spc) wasn't in xhemi/surf folder. How can I do that?
All best, Lanbo
On Mon, Nov 13, 2017 at 5:15 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
you can use anything that you can register the the FS anatomical
On 11/13/2017 04:34 PM, lanbo Wang wrote:
Can I use data processed by other tool like FSL, or I can only use DTI image after Freesurfer processing?
On Fri, Nov 10, 2017 at 3:07 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yes On 11/10/17 2:45 PM, lanbo Wang wrote:Thank you very much, it's work. I have another question, this is for structural imaging. Can I use those steps for fmri or DTI imaging? On Fri, Nov 10, 2017 at 1:08 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>wrote:
Don't use --conjunct, just mri_concat file1 file2 ... file N --o output On 11/10/17 12:56 PM, lanbo Wang wrote:I firstly did mris_preproc separately. Secondly used fscalc to reverse left symptom subjects. Thirdly used mri_concat --conjunct to combine all the subjects together. The code is: 1.mris_preproc --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.s02.mg <http://lh.lh-rh.thickness.sm00.s02.mg>h \ --s subj_02_1 2. fscalc lh.lh-rh.thickness.sm00.s09.mg <http://lh.lh-rh.thickness.sm00.s09.mg>h mul -1 -o lh.lh-rh.thickness.sm00.s09.mg <http://lh.lh-rh.thickness.sm00.s09.mg>h 3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mg <http://lh.lh-rh.thickness.sm00.s02.mg>h lh.lh-rh.thickness.sm00.s03.mg <http://lh.lh-rh.thickness.sm00.s03.mg>h lh.lh-rh.thickness.sm00.s04.mg <http://lh.lh-rh.thickness.sm00.s04.mg>h lh.lh-rh.thickness.sm00.s05.mg <http://lh.lh-rh.thickness.sm00.s05.mg>h lh.lh-rh.thickness.sm00.s06.mg <http://lh.lh-rh.thickness.sm00.s06.mg>h lh.lh-rh.thickness.sm00.s08.mg <http://lh.lh-rh.thickness.sm00.s08.mg>h lh.lh-rh.thickness.sm00.s09.mg <http://lh.lh-rh.thickness.sm00.s09.mg>h lh.lh-rh.thickness.sm00.s10.mg <http://lh.lh-rh.thickness.sm00.s10.mg>h lh.lh-rh.thickness.sm00.s11.mg <http://lh.lh-rh.thickness.sm00.s11.mg>h lh.lh-rh.thickness.sm00.s12.mg <http://lh.lh-rh.thickness.sm00.s12.mg>h lh.lh-rh.thickness.sm00.s13.mg <http://lh.lh-rh.thickness.sm00.s13.mg>h lh.lh-rh.thickness.sm00.s14.mg <http://lh.lh-rh.thickness.sm00.s14.mg>h lh.lh-rh.thickness.sm00.s15.mg <http://lh.lh-rh.thickness.sm00.s15.mg>h lh.lh-rh.thickness.sm00.s16.mg <http://lh.lh-rh.thickness.sm00.s16.mg>h lh.lh-rh.thickness.sm00.s17.mg <http://lh.lh-rh.thickness.sm00.s17.mg>h lh.lh-rh.thickness.sm00.s18.mg <http://lh.lh-rh.thickness.sm00.s18.mg>h lh.lh-rh.thickness.sm00.s19.mg <http://lh.lh-rh.thickness.sm00.s19.mg>h lh.lh-rh.thickness.sm00.s20.mg <http://lh.lh-rh.thickness.sm00.s20.mg>h lh.lh-rh.thickness.sm00.s21.mg <http://lh.lh-rh.thickness.sm00.s21.mg>h lh.lh-rh.thickness.sm00.s22.mg <http://lh.lh-rh.thickness.sm00.s22.mg>h lh.lh-rh.thickness.sm00.s24.mg <http://lh.lh-rh.thickness.sm00.s24.mg>h lh.lh-rh.thickness.sm00.s25.mg <http://lh.lh-rh.thickness.sm00.s25.mg>h lh.lh-rh.thickness.sm00.s26.mg <http://lh.lh-rh.thickness.sm00.s26.mg>h lh.lh-rh.thickness.sm00.s27.mg <http://lh.lh-rh.thickness.sm00.s27.mg>h lh.lh-rh.thickness.sm00.s29.mg <http://lh.lh-rh.thickness.sm00.s29.mg>h lh.lh-rh.thickness.sm00.s32.mg <http://lh.lh-rh.thickness.sm00.s32.mg>h --o lh.lh-rh.thickness.sm00.mgh 4.smooth 5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Do you only have one subject in your input file? You need to run mris_preproc separately for each subject, create a different file for each, then mri_concat the files together On 11/9/17 6:20 PM, lanbo Wang wrote:Dr. Douglas, I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white
Number of vertices 163842 Number of faces 327680 Total area 61972.710938 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh sysname Linux hostname localhost.localdomain machine x86_64 user mtobia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th
<http://lh.lh-rh.th>ickness.sm10.mgh logyflag 0 usedti 0 labelmask /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label
maskinv 0 glmdir glm.lh.lh-rh.thickness.sm10 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory glm.lh.lh-rh.thickness.sm10 Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th
<http://lh.lh-rh.th>ickness.sm10.mgh Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat
Normalized matrix condition is 1 Matrix condition is 1 Found 146902 points in label. Pruning voxels by thr: 0.000000 Found 146902 voxels in mask Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh Reshaping mriglm->mask... search space = 79288.081914 DOF = 0 ERROR: DOF = 0 The code I used before this one is How can I resolve this problem. Thanks, Lanbo On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: which code. I gave 3 options below, which one did you use? On 11/07/2017 02:43 PM, lanbo Wang wrote: > I try to use this code to compare left and right hemisphere by paired > t-test and add age as covariate. > > Thanks, > Lanbo > > On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > which method are you trying to implement? If #3, then you need to run > mris_preproc separately for each subject, and then run that fscalc > command > > > On 11/07/2017 11:33 AM, lanbo Wang wrote: > > Hi Douglas, > > > > Thanks for your reply. > > I created the fsgd file as you show me, and run code like this. Am I > > right? > > 1. > > mris_preproc --fsgd Subject.xhemi.dat \ > > --target fsaverage_sym --hemi lh \ > > --xhemi --paired-diff \ > > --srcsurfreg fsaverage_sym.sphere.reg \ > > --meas thickness \ > > --out lh.lh-rh.thickness.age.sm00.mg <http://lh.lh-rh.thickness.age.sm00.mg>h \ > > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s > > subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s > subj_12_1 > > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s > > subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s > subj_22_1 > > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s > > subj_29_1 --s subj_32_1 > > > > 2. > > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mg <http://lh.lh-rh.thickness.age.sm10.mg>h --glmdir > > glm.lh.lh-rh.thickness.age.sm10 \ > > --fsgd Subject.xhemi.dat \ > > --C Avg-thickness-age-Cor.mtx \ > > --surf fsaverage_sym lh > > > > Attachment is fsgd and Avg-thickness-age-cor.mtx. > > > > All best, > > Lanbo Wang > > > > > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: > > > > Hi Danny > > > > you need to give us more information if you want us to help you. > > Please include the command you ran and the entire screen output. > > > > cheers > > Bruce > > > > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > > > Dear FDs, > > I encountered an odd situation: > > > > My free surfer will always shut down when I run command. > > > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel > > Core i5 > > > > I don’t know if the compatibility is fine with my download > > version (MacOS Lion OS X 10.7 (64b > > intel)Stable v6.0.0) > > > > Please kindly suggest. > > > > Thanks ver much > > > > Best Regards,Danny Deng > > > > > > On Nov 7, 2017, at 7:14 AM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > wrote: > > > > > > > > On 11/06/2017 12:03 PM, lanbo Wang wrote: > > Dear experts, > > > > I have two questions about hemisphere analysis: > > > > 1) When I run left-right hemisphere paired t-test, > can I > > add age as > > covariate? If use fsgd to add covariate, to this > paired > > t-test > > analysis, how to make the fsgd table? > > > > use this one-group, one-covariate example > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V> > 2) I want to reorganize the hemisphere from > left-right to > > symptom-nosymptom according to body symptom side > record > > and compare > > different between symptom hemisphere and nosymptom > > hemisphere. Can I > > use freesurfer to do it? > > > > Yes, though it is a little tricky with multiple ways, each > > complicated > > in its own way. > > 1. Create your own design matrix. You can use the one > created by > > mri_glmfit to start. Assuming you want > > symptomHemi-nosymptomHemi, then, > > in each subject whose symptomHemi is rh, multiply its > line in > > the design > > matrix by -1. Then pass this design matrix to mri_glmfit > with --X > > instead of passing an FSGD file. > > 2. Load the output of mris_preproc into matlab, eg, y = > > MRIread('y.mgh');, then change the sign as in #1 above, eg, > > y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each > applicable > > subject. Then save the data with MRIwrite(y,'new.y.mgh');, > > then run > > mri_glmfit as normal with the new file. > > 3. Run mris_preproc for each subject separately to > generate an > > lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the > > sign as in > > #1 above with > > fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o > > lh.lh-rh.thickness.sm00.subject10.mgh > > Then run mri_concat to concatenate all the subjects together > > in the same > > order as they are listed in the FSGD file, then use this > stack > > as input > > the mri_glmfit > > > > > > Thanks for your patient and help. > > > > All best, > > Lanbo Wang > > > > > > ______________________________
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> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>
> > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>
> > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > > > > > 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 Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> . If the e-mail was > > sent to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > > > > > 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 Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> . If the e-mail was sent > > to you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > ______________________________
> > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:%28617%29%20724-2358> Fax: 617-726-7422 <tel:%28617%29%20726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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 Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Danny Deng -
Douglas Greve -
Douglas N Greve
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lanbo Wang