Hi All,
Although the question of flipping hemispheres has come up before, I still struggling with it. I'm working on a longitudinal study with stroke subjects (half with lh lesions, half with rh lesions). We want to compare only the non-lesioned, healthy, hemispheres at 2 timepoints (pre- and post-therapy).
Using the tutorial (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) as a guide, I've completed the longitudinal analysis (cross-base-long steps) for both lh- and rh-lesioned subjects.
I've done the thickness data qcache for the right/healthy hemi for the lh-lesioned group: long_mris_slopes --qdec long_qdec_lh_lesion_subjects_table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time my_time_var --qcache fsaverage_sym --sd $SUBJECTS_DIR
Convert the long_qdec_lh_lesion_subjects_table.dat into a cross.qdec.table.dat to use in qdec. This works well---I can look for clusters where athe average thickness-rate is different from 0.
How can I combine the rh-lesioned group with the first group?
I thought I could flip hemispheres of the results at each subject's longitudinal output timepoint with: surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
but this terminated with an error:
recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach
ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters:
\' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.
I know it's recommended to flip hemispheres after processing (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html). When (and how) is it best done?
Thanks, Peggy
You have uncovered a bug. I don't think anyone has tried to run xhemi on a longitudinal data set before. There is a work-around. First run
xhemireg --s subject --no-tal
Then run
surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
I think this should work
doug
On 03/14/2014 03:39 PM, Peggy Skelly wrote:
Hi All,
Although the question of flipping hemispheres has come up before, I still struggling with it. I'm working on a longitudinal study with stroke subjects (half with lh lesions, half with rh lesions). We want to compare only the non-lesioned, healthy, hemispheres at 2 timepoints (pre- and post-therapy).
Using the tutorial (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) as a guide, I've completed the longitudinal analysis (cross-base-long steps) for both lh- and rh-lesioned subjects.
I've done the thickness data qcache for the right/healthy hemi for the lh-lesioned group: long_mris_slopes --qdec long_qdec_lh_lesion_subjects_table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time my_time_var --qcache fsaverage_sym --sd $SUBJECTS_DIR
Convert the long_qdec_lh_lesion_subjects_table.dat into a cross.qdec.table.dat to use in qdec. This works well---I can look for clusters where athe average thickness-rate is different from 0.
How can I combine the rh-lesioned group with the first group?
I thought I could flip hemispheres of the results at each subject's longitudinal output timepoint with: surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
but this terminated with an error:
recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach
ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters:
\' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.I know it's recommended to flip hemispheres after processing (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html). When (and how) is it best done?
Thanks, Peggy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Actually, I don't think this will work. What version of FS are you running?
I've created a patch of the 5.3 recon-all here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
Copy this to $FREESURFER_HOME/bin/recon-all (after making a backup!)
then re-run
doug
On 03/14/2014 03:57 PM, Douglas N Greve wrote:
You have uncovered a bug. I don't think anyone has tried to run xhemi on a longitudinal data set before. There is a work-around. First run
xhemireg --s subject --no-tal
Then run
surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
I think this should work
doug
On 03/14/2014 03:39 PM, Peggy Skelly wrote:
Hi All,
Although the question of flipping hemispheres has come up before, I still struggling with it. I'm working on a longitudinal study with stroke subjects (half with lh lesions, half with rh lesions). We want to compare only the non-lesioned, healthy, hemispheres at 2 timepoints (pre- and post-therapy).
Using the tutorial (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) as a guide, I've completed the longitudinal analysis (cross-base-long steps) for both lh- and rh-lesioned subjects.
I've done the thickness data qcache for the right/healthy hemi for the lh-lesioned group: long_mris_slopes --qdec long_qdec_lh_lesion_subjects_table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time my_time_var --qcache fsaverage_sym --sd $SUBJECTS_DIR
Convert the long_qdec_lh_lesion_subjects_table.dat into a cross.qdec.table.dat to use in qdec. This works well---I can look for clusters where athe average thickness-rate is different from 0.
How can I combine the rh-lesioned group with the first group?
I thought I could flip hemispheres of the results at each subject's longitudinal output timepoint with: surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
but this terminated with an error:
recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach
ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters:
\' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.I know it's recommended to flip hemispheres after processing (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html). When (and how) is it best done?
Thanks, Peggy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks -- (I thought I might not have understood the processing pipeline properly.)
I'm running 5.3, I'll try the patch and let you know how it works.
Peggy
On 3/14/14, 16:07 , Douglas N Greve wrote:
Actually, I don't think this will work. What version of FS are you running?
I've created a patch of the 5.3 recon-all here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
Copy this to $FREESURFER_HOME/bin/recon-all (after making a backup!)
then re-run
doug
On 03/14/2014 03:57 PM, Douglas N Greve wrote:
You have uncovered a bug. I don't think anyone has tried to run xhemi on a longitudinal data set before. There is a work-around. First run
xhemireg --s subject --no-tal
Then run
surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
I think this should work
doug
On 03/14/2014 03:39 PM, Peggy Skelly wrote:
Hi All,
Although the question of flipping hemispheres has come up before, I still struggling with it. I'm working on a longitudinal study with stroke subjects (half with lh lesions, half with rh lesions). We want to compare only the non-lesioned, healthy, hemispheres at 2 timepoints (pre- and post-therapy).
Using the tutorial (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) as a guide, I've completed the longitudinal analysis (cross-base-long steps) for both lh- and rh-lesioned subjects.
I've done the thickness data qcache for the right/healthy hemi for the lh-lesioned group: long_mris_slopes --qdec long_qdec_lh_lesion_subjects_table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time my_time_var --qcache fsaverage_sym --sd $SUBJECTS_DIR
Convert the long_qdec_lh_lesion_subjects_table.dat into a cross.qdec.table.dat to use in qdec. This works well---I can look for clusters where athe average thickness-rate is different from 0.
How can I combine the rh-lesioned group with the first group?
I thought I could flip hemispheres of the results at each subject's longitudinal output timepoint with: surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
but this terminated with an error:
recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach
ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters:
\' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.I know it's recommended to flip hemispheres after processing (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html). When (and how) is it best done?
Thanks, Peggy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The patch works! Thank you.
Now, to compute the longitudinal measures: I don't see 'long_mris_slopes --help' mentioning xhemi, so I suppose it won't be able to find the flipped subjects. Is there a way to copy/rename the <subj>/xhemi/ directory to $SUBJECTS_DIR so I could run long_mris_slopes?
Peggy
On 3/14/14, 7:13 PM, Peggy Skelly wrote:
Thanks -- (I thought I might not have understood the processing pipeline properly.)
I'm running 5.3, I'll try the patch and let you know how it works.
Peggy
On 3/14/14, 16:07 , Douglas N Greve wrote:
Actually, I don't think this will work. What version of FS are you running?
I've created a patch of the 5.3 recon-all here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
Copy this to $FREESURFER_HOME/bin/recon-all (after making a backup!)
then re-run
doug
On 03/14/2014 03:57 PM, Douglas N Greve wrote:
You have uncovered a bug. I don't think anyone has tried to run xhemi on a longitudinal data set before. There is a work-around. First run
xhemireg --s subject --no-tal
Then run
surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
I think this should work
doug
On 03/14/2014 03:39 PM, Peggy Skelly wrote:
Hi All,
Although the question of flipping hemispheres has come up before, I still struggling with it. I'm working on a longitudinal study with stroke subjects (half with lh lesions, half with rh lesions). We want to compare only the non-lesioned, healthy, hemispheres at 2 timepoints (pre- and post-therapy).
Using the tutorial (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) as a guide, I've completed the longitudinal analysis (cross-base-long steps) for both lh- and rh-lesioned subjects.
I've done the thickness data qcache for the right/healthy hemi for the lh-lesioned group: long_mris_slopes --qdec long_qdec_lh_lesion_subjects_table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time my_time_var --qcache fsaverage_sym --sd $SUBJECTS_DIR
Convert the long_qdec_lh_lesion_subjects_table.dat into a cross.qdec.table.dat to use in qdec. This works well---I can look for clusters where athe average thickness-rate is different from 0.
How can I combine the rh-lesioned group with the first group?
I thought I could flip hemispheres of the results at each subject's longitudinal output timepoint with: surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
but this terminated with an error:
recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach
ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters:
\' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.I know it's recommended to flip hemispheres after processing (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html).
When (and how) is it best done?
Thanks, Peggy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm not sure this will work but try entering the subjectids in the qdec table as subjectTP and subjectTP/xhemi and use subject as the base (TP is just a shorthand for time point, use whatever you used) doug
On 03/17/2014 01:09 PM, Peggy Skelly wrote:
The patch works! Thank you.
Now, to compute the longitudinal measures: I don't see 'long_mris_slopes --help' mentioning xhemi, so I suppose it won't be able to find the flipped subjects. Is there a way to copy/rename the <subj>/xhemi/ directory to $SUBJECTS_DIR so I could run long_mris_slopes?
Peggy
On 3/14/14, 7:13 PM, Peggy Skelly wrote:
Thanks -- (I thought I might not have understood the processing pipeline properly.)
I'm running 5.3, I'll try the patch and let you know how it works.
Peggy
On 3/14/14, 16:07 , Douglas N Greve wrote:
Actually, I don't think this will work. What version of FS are you running?
I've created a patch of the 5.3 recon-all here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
Copy this to $FREESURFER_HOME/bin/recon-all (after making a backup!)
then re-run
doug
On 03/14/2014 03:57 PM, Douglas N Greve wrote:
You have uncovered a bug. I don't think anyone has tried to run xhemi on a longitudinal data set before. There is a work-around. First run
xhemireg --s subject --no-tal
Then run
surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
I think this should work
doug
On 03/14/2014 03:39 PM, Peggy Skelly wrote:
Hi All,
Although the question of flipping hemispheres has come up before, I still struggling with it. I'm working on a longitudinal study with stroke subjects (half with lh lesions, half with rh lesions). We want to compare only the non-lesioned, healthy, hemispheres at 2 timepoints (pre- and post-therapy).
Using the tutorial (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) as a guide, I've completed the longitudinal analysis (cross-base-long steps) for both lh- and rh-lesioned subjects.
I've done the thickness data qcache for the right/healthy hemi for the lh-lesioned group: long_mris_slopes --qdec long_qdec_lh_lesion_subjects_table.dat --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time my_time_var --qcache fsaverage_sym --sd $SUBJECTS_DIR
Convert the long_qdec_lh_lesion_subjects_table.dat into a cross.qdec.table.dat to use in qdec. This works well---I can look for clusters where athe average thickness-rate is different from 0.
How can I combine the rh-lesioned group with the first group?
I thought I could flip hemispheres of the results at each subject's longitudinal output timepoint with: surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
but this terminated with an error:
recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach
ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters:
\' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists.I know it's recommended to flip hemispheres after processing (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html).
When (and how) is it best done?
Thanks, Peggy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I tried your suggestion (using subjTP/xhemi in place of subjTP) in the qdec table. I doesn't work because long_mris_slopes uses subjTP and subjBase to create "subjTP.long.subjBase", the directory of the actual data. Extra slashes "/" in the name create an incorrect name (i.e. subjTP/xhemi.long.subjBase/xhemi).
So I tried copying the contents of the /xhemi subdirectories into a different $SUBJECTS_DIR with timepoint and base names the way long_mris_slopes expects them: subjdir_xhemi/subjTP1.long.subjbase subjdir_xhemi/subjTP2.long.subjbase subjdir_xhemi/subjbase
This works to create appropriate path/filenames for long_mris_slopes. But ...
The problem now is when long_mris_slopes calls mri_label2label (mapping cortex labels to fsaverage_sym), the file surf/rh.sphere.reg is not found. It's not in the /xhemi/surf directory. It is in the original subject directory. xhemi/surf/ only contains rh.fsaverage_sym.sphere.reg.
Any suggestions? Am I approaching this problem (combining healthy hemispheres in a longitudinal study) correctly?
Peggy
On Mon, Mar 17, 2014 at 3:35 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
I'm not sure this will work but try entering the subjectids in the qdec table as subjectTP and subjectTP/xhemi and use subject as the base (TP is just a shorthand for time point, use whatever you used) doug
On 03/17/2014 01:09 PM, Peggy Skelly wrote:
The patch works! Thank you.
Now, to compute the longitudinal measures: I don't see 'long_mris_slopes --help' mentioning xhemi, so I suppose it won't be able to find the flipped subjects. Is there a way to copy/rename the <subj>/xhemi/ directory to $SUBJECTS_DIR so I could run long_mris_slopes?
Peggy
On 3/14/14, 7:13 PM, Peggy Skelly wrote:
Thanks -- (I thought I might not have understood the processing pipeline properly.)
I'm running 5.3, I'll try the patch and let you know how it works.
Peggy
On 3/14/14, 16:07 , Douglas N Greve wrote:
Actually, I don't think this will work. What version of FS are you running?
I've created a patch of the 5.3 recon-all here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
Copy this to $FREESURFER_HOME/bin/recon-all (after making a backup!)
then re-run
doug
On 03/14/2014 03:57 PM, Douglas N Greve wrote:
You have uncovered a bug. I don't think anyone has tried to run xhemi on a longitudinal data set before. There is a work-around. First run
xhemireg --s subject --no-tal
Then run
surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
I think this should work
doug
On 03/14/2014 03:39 PM, Peggy Skelly wrote:
Hi All,
Although the question of flipping hemispheres has come up before, I still struggling with it. I'm working on a longitudinal study with stroke subjects (half with
lh
lesions, half with rh lesions). We want to compare only the non-lesioned, healthy, hemispheres at 2 timepoints (pre- and post-therapy).
Using the tutorial (
http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview)
as a guide, I've completed the longitudinal analysis (cross-base-long steps) for both lh- and rh-lesioned subjects.
I've done the thickness data qcache for the right/healthy hemi for
the
lh-lesioned group: long_mris_slopes --qdec long_qdec_lh_lesion_subjects_table.dat
--meas
thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time my_time_var --qcache fsaverage_sym --sd $SUBJECTS_DIR
Convert the long_qdec_lh_lesion_subjects_table.dat into a cross.qdec.table.dat to use in qdec. This works well---I can look for clusters where athe average thickness-rate is different from 0.
How can I combine the rh-lesioned group with the first group?
I thought I could flip hemispheres of the results at each subject's longitudinal output timepoint with: surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi
but this terminated with an error: > recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach > > ERROR: Are you trying to run or re-run a longitudinal time point? > If so, please specify the following parameters: > > ' -long <tpNid> <templateid> ' > > where <tpNid> is the time point id (SAME as cross
sectional
> ID) and <templateid> is the ID created in the -base run. > The directory <tpNid>.long.<templateid> will be created > automatically or used for output, if it already exists. I know it's recommended to flip hemispheres after processing (
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html ).
When (and how) is it best done?
Thanks, Peggy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
mri_label2label needs to be called with --surfreg fsaverage_sym.sphere.reg
Martin, can you modify long_mris_slopes to add this?
But another question is exactly what you want to do in the end. What function of the slopes and hemisphere are you trying to compute?
doug
On 03/21/2014 01:20 PM, Peggy Skelly wrote:
I tried your suggestion (using subjTP/xhemi in place of subjTP) in the qdec table. I doesn't work because long_mris_slopes uses subjTP and subjBase to create "subjTP.long.subjBase", the directory of the actual data. Extra slashes "/" in the name create an incorrect name (i.e. subjTP/xhemi.long.subjBase/xhemi).
So I tried copying the contents of the /xhemi subdirectories into a different $SUBJECTS_DIR with timepoint and base names the way long_mris_slopes expects them: subjdir_xhemi/subjTP1.long.subjbase subjdir_xhemi/subjTP2.long.subjbase subjdir_xhemi/subjbase
This works to create appropriate path/filenames for long_mris_slopes. But ...
The problem now is when long_mris_slopes calls mri_label2label (mapping cortex labels to fsaverage_sym), the file surf/rh.sphere.reg is not found. It's not in the /xhemi/surf directory. It is in the original subject directory. xhemi/surf/ only contains rh.fsaverage_sym.sphere.reg.
Any suggestions? Am I approaching this problem (combining healthy hemispheres in a longitudinal study) correctly?
Peggy
On Mon, Mar 17, 2014 at 3:35 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I'm not sure this will work but try entering the subjectids in the qdec table as subjectTP and subjectTP/xhemi and use subject as the base (TP is just a shorthand for time point, use whatever you used) doug On 03/17/2014 01:09 PM, Peggy Skelly wrote: > The patch works! Thank you. > > Now, to compute the longitudinal measures: I don't see 'long_mris_slopes > --help' mentioning xhemi, so I suppose > it won't be able to find the flipped subjects. Is there a way to > copy/rename the <subj>/xhemi/ directory > to $SUBJECTS_DIR so I could run long_mris_slopes? > > Peggy > > On 3/14/14, 7:13 PM, Peggy Skelly wrote: >> Thanks -- (I thought I might not have understood the processing >> pipeline properly.) >> >> I'm running 5.3, I'll try the patch and let you know how it works. >> >> Peggy >> >> >> On 3/14/14, 16:07 , Douglas N Greve wrote: >>> Actually, I don't think this will work. What version of FS are you >>> running? >>> >>> I've created a patch of the 5.3 recon-all here >>> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch >>> >>> >>> Copy this to $FREESURFER_HOME/bin/recon-all (after making a backup!) >>> >>> then re-run >>> >>> doug >>> >>> >>> On 03/14/2014 03:57 PM, Douglas N Greve wrote: >>>> You have uncovered a bug. I don't think anyone has tried to run >>>> xhemi on >>>> a longitudinal data set before. There is a work-around. First run >>>> >>>> xhemireg --s subject --no-tal >>>> >>>> Then run >>>> >>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi >>>> >>>> I think this should work >>>> >>>> doug >>>> >>>> >>>> On 03/14/2014 03:39 PM, Peggy Skelly wrote: >>>>> Hi All, >>>>> >>>>> Although the question of flipping hemispheres has come up before, I >>>>> still struggling with it. >>>>> I'm working on a longitudinal study with stroke subjects (half with lh >>>>> lesions, half with rh lesions). We want to compare only the >>>>> non-lesioned, healthy, hemispheres at 2 timepoints (pre- and >>>>> post-therapy). >>>>> >>>>> Using the tutorial >>>>> (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) >>>>> as >>>>> a guide, I've completed the longitudinal analysis (cross-base-long >>>>> steps) for both lh- and rh-lesioned subjects. >>>>> >>>>> I've done the thickness data qcache for the right/healthy hemi for the >>>>> lh-lesioned group: >>>>> long_mris_slopes --qdec long_qdec_lh_lesion_subjects_table.dat --meas >>>>> thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack >>>>> --do-label --time my_time_var --qcache fsaverage_sym --sd >>>>> $SUBJECTS_DIR >>>>> >>>>> Convert the long_qdec_lh_lesion_subjects_table.dat into a >>>>> cross.qdec.table.dat to use in qdec. This works well---I can look for >>>>> clusters where athe average thickness-rate is different from 0. >>>>> >>>>> How can I combine the rh-lesioned group with the first group? >>>>> >>>>> I thought I could flip hemispheres of the results at each subject's >>>>> longitudinal output timepoint with: >>>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi >>>>> >>>>> but this terminated with an error: >>>>>> recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach >>>>>> >>>>>> ERROR: Are you trying to run or re-run a longitudinal time point? >>>>>> If so, please specify the following parameters: >>>>>> >>>>>> \' -long <tpNid> <templateid> \' >>>>>> >>>>>> where <tpNid> is the time point id (SAME as cross sectional >>>>>> ID) and <templateid> is the ID created in the -base run. >>>>>> The directory <tpNid>.long.<templateid> will be created >>>>>> automatically or used for output, if it already exists. >>>>> I know it's recommended to flip hemispheres after processing >>>>> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html). >>>>> >>>>> When (and how) is it best done? >>>>> >>>>> Thanks, >>>>> Peggy >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> 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 > > -- 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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. 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The overall question is: did the cortical thickness of healthy hemispheres (of stroke subjects) change from tp1 to tp2, and does it correlate with the change in their functional measure? So I was using the long.thickness-rate measure and qdec.
Peggy
On Fri, Mar 21, 2014 at 1:38 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
mri_label2label needs to be called with --surfreg fsaverage_sym.sphere.reg
Martin, can you modify long_mris_slopes to add this?
But another question is exactly what you want to do in the end. What function of the slopes and hemisphere are you trying to compute?
doug
On 03/21/2014 01:20 PM, Peggy Skelly wrote:
I tried your suggestion (using subjTP/xhemi in place of subjTP) in the qdec table. I doesn't work because long_mris_slopes uses subjTP and subjBase to create "subjTP.long.subjBase", the directory of the actual data. Extra slashes "/" in the name create an incorrect name (i.e. subjTP/xhemi.long.subjBase/xhemi).
So I tried copying the contents of the /xhemi subdirectories into a different $SUBJECTS_DIR with timepoint and base names the way long_mris_slopes expects them: subjdir_xhemi/subjTP1.long.subjbase subjdir_xhemi/subjTP2.long.subjbase subjdir_xhemi/subjbase
This works to create appropriate path/filenames for long_mris_slopes. But ...
The problem now is when long_mris_slopes calls mri_label2label (mapping cortex labels to fsaverage_sym), the file surf/rh.sphere.reg is not found. It's not in the /xhemi/surf directory. It is in the original subject directory. xhemi/surf/ only contains rh.fsaverage_sym.sphere.reg.
Any suggestions? Am I approaching this problem (combining healthy hemispheres in a longitudinal study) correctly?
Peggy
On Mon, Mar 17, 2014 at 3:35 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I'm not sure this will work but try entering the subjectids in the qdec table as subjectTP and subjectTP/xhemi and use subject as the base(TP
is just a shorthand for time point, use whatever you used) doug On 03/17/2014 01:09 PM, Peggy Skelly wrote: > The patch works! Thank you. > > Now, to compute the longitudinal measures: I don't see 'long_mris_slopes > --help' mentioning xhemi, so I suppose > it won't be able to find the flipped subjects. Is there a way to > copy/rename the <subj>/xhemi/ directory > to $SUBJECTS_DIR so I could run long_mris_slopes? > > Peggy > > On 3/14/14, 7:13 PM, Peggy Skelly wrote: >> Thanks -- (I thought I might not have understood the processing >> pipeline properly.) >> >> I'm running 5.3, I'll try the patch and let you know how it works. >> >> Peggy >> >> >> On 3/14/14, 16:07 , Douglas N Greve wrote: >>> Actually, I don't think this will work. What version of FS areyou
>>> running? >>> >>> I've created a patch of the 5.3 recon-all here >>> >>>ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
>>> >>> >>> Copy this to $FREESURFER_HOME/bin/recon-all (after making a backup!) >>> >>> then re-run >>> >>> doug >>> >>> >>> On 03/14/2014 03:57 PM, Douglas N Greve wrote: >>>> You have uncovered a bug. I don't think anyone has tried to run >>>> xhemi on >>>> a longitudinal data set before. There is a work-around. Firstrun
>>>> >>>> xhemireg --s subject --no-tal >>>> >>>> Then run >>>> >>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi >>>> >>>> I think this should work >>>> >>>> doug >>>> >>>> >>>> On 03/14/2014 03:39 PM, Peggy Skelly wrote: >>>>> Hi All, >>>>> >>>>> Although the question of flipping hemispheres has come up before, I >>>>> still struggling with it. >>>>> I'm working on a longitudinal study with stroke subjects (half with lh >>>>> lesions, half with rh lesions). We want to compare only the >>>>> non-lesioned, healthy, hemispheres at 2 timepoints (pre- and >>>>> post-therapy). >>>>> >>>>> Using the tutorial >>>>> (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview)
>>>>> as >>>>> a guide, I've completed the longitudinal analysis (cross-base-long >>>>> steps) for both lh- and rh-lesioned subjects. >>>>> >>>>> I've done the thickness data qcache for the right/healthy hemi for the >>>>> lh-lesioned group: >>>>> long_mris_slopes --qdec long_qdec_lh_lesion_subjects_table.dat --meas >>>>> thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack >>>>> --do-label --time my_time_var --qcache fsaverage_sym --sd >>>>> $SUBJECTS_DIR >>>>> >>>>> Convert the long_qdec_lh_lesion_subjects_table.dat into a >>>>> cross.qdec.table.dat to use in qdec. This works well---I can look for >>>>> clusters where athe average thickness-rate is different from 0. >>>>> >>>>> How can I combine the rh-lesioned group with the first group? >>>>> >>>>> I thought I could flip hemispheres of the results at each subject's >>>>> longitudinal output timepoint with: >>>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh --xhemi >>>>> >>>>> but this terminated with an error: >>>>>> recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi -talairach >>>>>> >>>>>> ERROR: Are you trying to run or re-run a longitudinal time point? >>>>>> If so, please specify the following parameters: >>>>>> >>>>>> \' -long <tpNid> <templateid> \' >>>>>> >>>>>> where <tpNid> is the time point id (SAME as cross sectional >>>>>> ID) and <templateid> is the ID created in the -base run. >>>>>> The directory <tpNid>.long.<templateid> will be created >>>>>> automatically or used for output, if it already exists. >>>>> I know it's recommended to flip hemispheres after processing >>>>> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html ).
>>>>> >>>>> When (and how) is it best done? >>>>> >>>>> Thanks, >>>>> Peggy >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> 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 > > -- 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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Is the time between tp1 and tp2 the same for all subjects? If not, are you using that information?
On 03/21/2014 04:15 PM, Peggy Skelly wrote:
The overall question is: did the cortical thickness of healthy hemispheres (of stroke subjects) change from tp1 to tp2, and does it correlate with the change in their functional measure? So I was using the long.thickness-rate measure and qdec.
Peggy
On Fri, Mar 21, 2014 at 1:38 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
mri_label2label needs to be called with --surfreg fsaverage_sym.sphere.reg Martin, can you modify long_mris_slopes to add this? But another question is exactly what you want to do in the end. What function of the slopes and hemisphere are you trying to compute? doug On 03/21/2014 01:20 PM, Peggy Skelly wrote: > I tried your suggestion (using subjTP/xhemi in place of subjTP) in the > qdec table. I doesn't work because long_mris_slopes uses subjTP and > subjBase to create "subjTP.long.subjBase", the directory of the actual > data. Extra slashes "/" in the name create an incorrect name (i.e. > subjTP/xhemi.long.subjBase/xhemi). > > So I tried copying the contents of the /xhemi subdirectories into a > different $SUBJECTS_DIR with timepoint and base names the way > long_mris_slopes expects them: > subjdir_xhemi/subjTP1.long.subjbase > subjdir_xhemi/subjTP2.long.subjbase > subjdir_xhemi/subjbase > > This works to create appropriate path/filenames for long_mris_slopes. > But ... > > The problem now is when long_mris_slopes calls mri_label2label > (mapping cortex labels to fsaverage_sym), the file surf/rh.sphere.reg > is not found. It's not in the /xhemi/surf directory. It is in the > original subject directory. xhemi/surf/ only > contains rh.fsaverage_sym.sphere.reg. > > Any suggestions? Am I approaching this problem (combining healthy > hemispheres in a longitudinal study) correctly? > > Peggy > > > > On Mon, Mar 17, 2014 at 3:35 PM, 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: > > > I'm not sure this will work but try entering the subjectids in the > qdec > table as subjectTP and subjectTP/xhemi and use subject as the base (TP > is just a shorthand for time point, use whatever you used) > doug > > On 03/17/2014 01:09 PM, Peggy Skelly wrote: > > The patch works! Thank you. > > > > Now, to compute the longitudinal measures: I don't see > 'long_mris_slopes > > --help' mentioning xhemi, so I suppose > > it won't be able to find the flipped subjects. Is there a way to > > copy/rename the <subj>/xhemi/ directory > > to $SUBJECTS_DIR so I could run long_mris_slopes? > > > > Peggy > > > > On 3/14/14, 7:13 PM, Peggy Skelly wrote: > >> Thanks -- (I thought I might not have understood the processing > >> pipeline properly.) > >> > >> I'm running 5.3, I'll try the patch and let you know how it works. > >> > >> Peggy > >> > >> > >> On 3/14/14, 16:07 , Douglas N Greve wrote: > >>> Actually, I don't think this will work. What version of FS are you > >>> running? > >>> > >>> I've created a patch of the 5.3 recon-all here > >>> > >>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch > >>> > >>> > >>> Copy this to $FREESURFER_HOME/bin/recon-all (after making a > backup!) > >>> > >>> then re-run > >>> > >>> doug > >>> > >>> > >>> On 03/14/2014 03:57 PM, Douglas N Greve wrote: > >>>> You have uncovered a bug. I don't think anyone has tried to run > >>>> xhemi on > >>>> a longitudinal data set before. There is a work-around. First run > >>>> > >>>> xhemireg --s subject --no-tal > >>>> > >>>> Then run > >>>> > >>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh > --xhemi > >>>> > >>>> I think this should work > >>>> > >>>> doug > >>>> > >>>> > >>>> On 03/14/2014 03:39 PM, Peggy Skelly wrote: > >>>>> Hi All, > >>>>> > >>>>> Although the question of flipping hemispheres has come up > before, I > >>>>> still struggling with it. > >>>>> I'm working on a longitudinal study with stroke subjects > (half with lh > >>>>> lesions, half with rh lesions). We want to compare only the > >>>>> non-lesioned, healthy, hemispheres at 2 timepoints (pre- and > >>>>> post-therapy). > >>>>> > >>>>> Using the tutorial > >>>>> > (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) > >>>>> as > >>>>> a guide, I've completed the longitudinal analysis > (cross-base-long > >>>>> steps) for both lh- and rh-lesioned subjects. > >>>>> > >>>>> I've done the thickness data qcache for the right/healthy > hemi for the > >>>>> lh-lesioned group: > >>>>> long_mris_slopes --qdec > long_qdec_lh_lesion_subjects_table.dat --meas > >>>>> thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc > --do-stack > >>>>> --do-label --time my_time_var --qcache fsaverage_sym --sd > >>>>> $SUBJECTS_DIR > >>>>> > >>>>> Convert the long_qdec_lh_lesion_subjects_table.dat into a > >>>>> cross.qdec.table.dat to use in qdec. This works well---I can > look for > >>>>> clusters where athe average thickness-rate is different from 0. > >>>>> > >>>>> How can I combine the rh-lesioned group with the first group? > >>>>> > >>>>> I thought I could flip hemispheres of the results at each > subject's > >>>>> longitudinal output timepoint with: > >>>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh > --xhemi > >>>>> > >>>>> but this terminated with an error: > >>>>>> recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi > -talairach > >>>>>> > >>>>>> ERROR: Are you trying to run or re-run a longitudinal time > point? > >>>>>> If so, please specify the following parameters: > >>>>>> > >>>>>> \' -long <tpNid> <templateid> \' > >>>>>> > >>>>>> where <tpNid> is the time point id (SAME as cross > sectional > >>>>>> ID) and <templateid> is the ID created in the > -base run. > >>>>>> The directory <tpNid>.long.<templateid> will be > created > >>>>>> automatically or used for output, if it already > exists. > >>>>> I know it's recommended to flip hemispheres after processing > >>>>> > (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html). > >>>>> > >>>>> When (and how) is it best done? > >>>>> > >>>>> Thanks, > >>>>> Peggy > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> 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 > > _______________________________________________ > > 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 > > > > > > -- > 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> > FileDrop: 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> > Outgoing: > 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 > > > 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 <mailto: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 <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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The actual time between tp1 & tp2 varies for subjects, *but* every subject received the same "dose" of treatment between timepoints. To ask if the treatment changed a subject's cortical thickness, I'm not using the actual time difference, I'm using a constant 1 for the time difference. (i.e. in long.qdec.table tp1's time = 0, and tp2's time = 1 for all subjects.)
On Fri, Mar 21, 2014 at 4:44 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Is the time between tp1 and tp2 the same for all subjects? If not, are you using that information?
On 03/21/2014 04:15 PM, Peggy Skelly wrote:
The overall question is: did the cortical thickness of healthy hemispheres (of stroke subjects) change from tp1 to tp2, and does it correlate with the change in their functional measure? So I was using the long.thickness-rate measure and qdec.
Peggy
On Fri, Mar 21, 2014 at 1:38 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
mri_label2label needs to be called with --surfreg fsaverage_sym.sphere.reg Martin, can you modify long_mris_slopes to add this? But another question is exactly what you want to do in the end. What function of the slopes and hemisphere are you trying to compute? doug On 03/21/2014 01:20 PM, Peggy Skelly wrote: > I tried your suggestion (using subjTP/xhemi in place of subjTP) in the > qdec table. I doesn't work because long_mris_slopes uses subjTP and > subjBase to create "subjTP.long.subjBase", the directory of the actual > data. Extra slashes "/" in the name create an incorrect name (i.e. > subjTP/xhemi.long.subjBase/xhemi). > > So I tried copying the contents of the /xhemi subdirectories into a > different $SUBJECTS_DIR with timepoint and base names the way > long_mris_slopes expects them: > subjdir_xhemi/subjTP1.long.subjbase > subjdir_xhemi/subjTP2.long.subjbase > subjdir_xhemi/subjbase > > This works to create appropriate path/filenames for long_mris_slopes. > But ... > > The problem now is when long_mris_slopes calls mri_label2label > (mapping cortex labels to fsaverage_sym), the file surf/rh.sphere.reg > is not found. It's not in the /xhemi/surf directory. It is in the > original subject directory. xhemi/surf/ only > contains rh.fsaverage_sym.sphere.reg. > > Any suggestions? Am I approaching this problem (combining healthy > hemispheres in a longitudinal study) correctly? > > Peggy > > > > On Mon, Mar 17, 2014 at 3:35 PM, 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: > > > I'm not sure this will work but try entering the subjectids in the > qdec > table as subjectTP and subjectTP/xhemi and use subject as the base (TP > is just a shorthand for time point, use whatever you used) > doug > > On 03/17/2014 01:09 PM, Peggy Skelly wrote: > > The patch works! Thank you. > > > > Now, to compute the longitudinal measures: I don't see > 'long_mris_slopes > > --help' mentioning xhemi, so I suppose > > it won't be able to find the flipped subjects. Is there a way to > > copy/rename the <subj>/xhemi/ directory > > to $SUBJECTS_DIR so I could run long_mris_slopes? > > > > Peggy > > > > On 3/14/14, 7:13 PM, Peggy Skelly wrote: > >> Thanks -- (I thought I might not have understood the processing > >> pipeline properly.) > >> > >> I'm running 5.3, I'll try the patch and let you know how it works. > >> > >> Peggy > >> > >> > >> On 3/14/14, 16:07 , Douglas N Greve wrote: > >>> Actually, I don't think this will work. What version of FS are you > >>> running? > >>> > >>> I've created a patch of the 5.3 recon-all here > >>> > >>> >ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch
> >>> > >>> > >>> Copy this to $FREESURFER_HOME/bin/recon-all (after making a > backup!) > >>> > >>> then re-run > >>> > >>> doug > >>> > >>> > >>> On 03/14/2014 03:57 PM, Douglas N Greve wrote: > >>>> You have uncovered a bug. I don't think anyone has tried to run > >>>> xhemi on > >>>> a longitudinal data set before. There is a work-around. First run > >>>> > >>>> xhemireg --s subject --no-tal > >>>> > >>>> Then run > >>>> > >>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh > --xhemi > >>>> > >>>> I think this should work > >>>> > >>>> doug > >>>> > >>>> > >>>> On 03/14/2014 03:39 PM, Peggy Skelly wrote: > >>>>> Hi All, > >>>>> > >>>>> Although the question of flipping hemispheres has come up > before, I > >>>>> still struggling with it. > >>>>> I'm working on a longitudinal study with stroke subjects > (half with lh > >>>>> lesions, half with rh lesions). We want to compare only the > >>>>> non-lesioned, healthy, hemispheres at 2 timepoints (pre- and > >>>>> post-therapy). > >>>>> > >>>>> Using the tutorial > >>>>> > (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview)
> >>>>> as > >>>>> a guide, I've completed the longitudinal analysis > (cross-base-long > >>>>> steps) for both lh- and rh-lesioned subjects. > >>>>> > >>>>> I've done the thickness data qcache for the right/healthy > hemi for the > >>>>> lh-lesioned group: > >>>>> long_mris_slopes --qdec > long_qdec_lh_lesion_subjects_table.dat --meas > >>>>> thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc > --do-stack > >>>>> --do-label --time my_time_var --qcache fsaverage_sym --sd > >>>>> $SUBJECTS_DIR > >>>>> > >>>>> Convert the long_qdec_lh_lesion_subjects_table.dat into a > >>>>> cross.qdec.table.dat to use in qdec. This works well---I can > look for > >>>>> clusters where athe average thickness-rate is different from 0. > >>>>> > >>>>> How can I combine the rh-lesioned group with the first group? > >>>>> > >>>>> I thought I could flip hemispheres of the results at each > subject's > >>>>> longitudinal output timepoint with: > >>>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym --rh > --xhemi > >>>>> > >>>>> but this terminated with an error: > >>>>>> recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi > -talairach > >>>>>> > >>>>>> ERROR: Are you trying to run or re-run a longitudinal time > point? > >>>>>> If so, please specify the followingparameters:
> >>>>>> > >>>>>> \' -long <tpNid> <templateid> \' > >>>>>> > >>>>>> where <tpNid> is the time point id (SAME as cross > sectional > >>>>>> ID) and <templateid> is the ID created in the > -base run. > >>>>>> The directory <tpNid>.long.<templateid> willbe
> created > >>>>>> automatically or used for output, if italready
> exists. > >>>>> I know it's recommended to flip hemispheres after processing > >>>>> > (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html ).
> >>>>> > >>>>> When (and how) is it best done? > >>>>> > >>>>> Thanks, > >>>>> Peggy > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> 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 > > _______________________________________________ > > 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 > > > > > > -- > 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> > FileDrop: 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> > Outgoing: > 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 > > > 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 <mailto: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 <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 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/ _______________________________________________ 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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In that case, you can just do a paired analysis. Do a search for that on the wiki and you'll find examples doug
On 3/21/14 5:50 PM, Peggy Skelly wrote:
The actual time between tp1 & tp2 varies for subjects, *but* every subject received the same "dose" of treatment between timepoints. To ask if the treatment changed a subject's cortical thickness, I'm not using the actual time difference, I'm using a constant 1 for the time difference. (i.e. in long.qdec.table tp1's time = 0, and tp2's time = 1 for all subjects.)
On Fri, Mar 21, 2014 at 4:44 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Is the time between tp1 and tp2 the same for all subjects? If not, are you using that information? On 03/21/2014 04:15 PM, Peggy Skelly wrote: > The overall question is: did the cortical thickness of healthy > hemispheres (of stroke subjects) change from tp1 to tp2, and does it > correlate with the change in their functional measure? So I was using > the long.thickness-rate measure and qdec. > > Peggy > > > On Fri, Mar 21, 2014 at 1:38 PM, 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: > > > mri_label2label needs to be called with --surfreg > fsaverage_sym.sphere.reg > > Martin, can you modify long_mris_slopes to add this? > > But another question is exactly what you want to do in the end. What > function of the slopes and hemisphere are you trying to compute? > > doug > > > On 03/21/2014 01:20 PM, Peggy Skelly wrote: > > I tried your suggestion (using subjTP/xhemi in place of subjTP) > in the > > qdec table. I doesn't work because long_mris_slopes uses subjTP and > > subjBase to create "subjTP.long.subjBase", the directory of the > actual > > data. Extra slashes "/" in the name create an incorrect name (i.e. > > subjTP/xhemi.long.subjBase/xhemi). > > > > So I tried copying the contents of the /xhemi subdirectories into a > > different $SUBJECTS_DIR with timepoint and base names the way > > long_mris_slopes expects them: > > subjdir_xhemi/subjTP1.long.subjbase > > subjdir_xhemi/subjTP2.long.subjbase > > subjdir_xhemi/subjbase > > > > This works to create appropriate path/filenames for > long_mris_slopes. > > But ... > > > > The problem now is when long_mris_slopes calls mri_label2label > > (mapping cortex labels to fsaverage_sym), the file > surf/rh.sphere.reg > > is not found. It's not in the /xhemi/surf directory. It is in the > > original subject directory. xhemi/surf/ only > > contains rh.fsaverage_sym.sphere.reg. > > > > Any suggestions? Am I approaching this problem (combining healthy > > hemispheres in a longitudinal study) correctly? > > > > Peggy > > > > > > > > On Mon, Mar 17, 2014 at 3:35 PM, 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: > > > > > > I'm not sure this will work but try entering the subjectids > in the > > qdec > > table as subjectTP and subjectTP/xhemi and use subject as > the base (TP > > is just a shorthand for time point, use whatever you used) > > doug > > > > On 03/17/2014 01:09 PM, Peggy Skelly wrote: > > > The patch works! Thank you. > > > > > > Now, to compute the longitudinal measures: I don't see > > 'long_mris_slopes > > > --help' mentioning xhemi, so I suppose > > > it won't be able to find the flipped subjects. Is there a > way to > > > copy/rename the <subj>/xhemi/ directory > > > to $SUBJECTS_DIR so I could run long_mris_slopes? > > > > > > Peggy > > > > > > On 3/14/14, 7:13 PM, Peggy Skelly wrote: > > >> Thanks -- (I thought I might not have understood the > processing > > >> pipeline properly.) > > >> > > >> I'm running 5.3, I'll try the patch and let you know how > it works. > > >> > > >> Peggy > > >> > > >> > > >> On 3/14/14, 16:07 , Douglas N Greve wrote: > > >>> Actually, I don't think this will work. What version of > FS are you > > >>> running? > > >>> > > >>> I've created a patch of the 5.3 recon-all here > > >>> > > >>> > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/recon-all.53.patch > > >>> > > >>> > > >>> Copy this to $FREESURFER_HOME/bin/recon-all (after making a > > backup!) > > >>> > > >>> then re-run > > >>> > > >>> doug > > >>> > > >>> > > >>> On 03/14/2014 03:57 PM, Douglas N Greve wrote: > > >>>> You have uncovered a bug. I don't think anyone has > tried to run > > >>>> xhemi on > > >>>> a longitudinal data set before. There is a work-around. > First run > > >>>> > > >>>> xhemireg --s subject --no-tal > > >>>> > > >>>> Then run > > >>>> > > >>>> surfreg --s subj1_Tp1.long.subj1_base --t fsaverage_sym > --rh > > --xhemi > > >>>> > > >>>> I think this should work > > >>>> > > >>>> doug > > >>>> > > >>>> > > >>>> On 03/14/2014 03:39 PM, Peggy Skelly wrote: > > >>>>> Hi All, > > >>>>> > > >>>>> Although the question of flipping hemispheres has come up > > before, I > > >>>>> still struggling with it. > > >>>>> I'm working on a longitudinal study with stroke subjects > > (half with lh > > >>>>> lesions, half with rh lesions). We want to compare > only the > > >>>>> non-lesioned, healthy, hemispheres at 2 timepoints > (pre- and > > >>>>> post-therapy). > > >>>>> > > >>>>> Using the tutorial > > >>>>> > > > (http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial_freeview) > > >>>>> as > > >>>>> a guide, I've completed the longitudinal analysis > > (cross-base-long > > >>>>> steps) for both lh- and rh-lesioned subjects. > > >>>>> > > >>>>> I've done the thickness data qcache for the right/healthy > > hemi for the > > >>>>> lh-lesioned group: > > >>>>> long_mris_slopes --qdec > > long_qdec_lh_lesion_subjects_table.dat --meas > > >>>>> thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc > > --do-stack > > >>>>> --do-label --time my_time_var --qcache fsaverage_sym --sd > > >>>>> $SUBJECTS_DIR > > >>>>> > > >>>>> Convert the long_qdec_lh_lesion_subjects_table.dat into a > > >>>>> cross.qdec.table.dat to use in qdec. This works > well---I can > > look for > > >>>>> clusters where athe average thickness-rate is > different from 0. > > >>>>> > > >>>>> How can I combine the rh-lesioned group with the first > group? > > >>>>> > > >>>>> I thought I could flip hemispheres of the results at each > > subject's > > >>>>> longitudinal output timepoint with: > > >>>>> surfreg --s subj1_Tp1.long.subj1_base --t > fsaverage_sym --rh > > --xhemi > > >>>>> > > >>>>> but this terminated with an error: > > >>>>>> recon-all -sb s1311_15T_post.long.s1311_15T_base/xhemi > > -talairach > > >>>>>> > > >>>>>> ERROR: Are you trying to run or re-run a longitudinal > time > > point? > > >>>>>> If so, please specify the following parameters: > > >>>>>> > > >>>>>> \' -long <tpNid> <templateid> \' > > >>>>>> > > >>>>>> where <tpNid> is the time point id (SAME as > cross > > sectional > > >>>>>> ID) and <templateid> is the ID created in the > > -base run. > > >>>>>> The directory <tpNid>.long.<templateid> will be > > created > > >>>>>> automatically or used for output, if it already > > exists. > > >>>>> I know it's recommended to flip hemispheres after > processing > > >>>>> > > > (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html). > > >>>>> > > >>>>> When (and how) is it best done? > > >>>>> > > >>>>> Thanks, > > >>>>> Peggy > > >>>>> > > >>>>> > > >>>>> > > >>>>> _______________________________________________ > > >>>>> 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 > > > _______________________________________________ > > > 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 > > > > > > > > > > -- > > 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> > > FileDrop: 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/ > > > > _______________________________________________ > > 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 > > > > > > 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 <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 > > -- > 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> > FileDrop: 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> > Outgoing: > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Douglas Greve -
Douglas N Greve
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Peggy Skelly