Hi FreeSurfer folks:
I am trying to extract LGI values from Brodmann Areas 44 and 45. I am using the following script. Unfortunately it gives me an error message. Could you please help me.
aparcstats2table --skip -s /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --hemi lh --parc=BA --meas foldind --tablefile BA44 BA45 -lh.BA.stats --subjectsfile=BA_LGI.txt
thanks so much,
Alan Francis
Hi Alan, it would be a lot easier to help if you told us what the error msg is:). Please supply the full terminal output including error msg. thanks doug
On 09/03/2013 10:52 AM, Alan Francis wrote:
Hi FreeSurfer folks:
I am trying to extract LGI values from Brodmann Areas 44 and 45. I am using the following script. Unfortunately it gives me an error message. Could you please help me.
aparcstats2table --skip -s /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --hemi lh --parc=BA --meas foldind --tablefile BA44 BA45 -lh.BA.stats --subjectsfile=BA_LGI.txt
thanks so much,
Alan Francis
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug:
Here is the message it gives. It's not so much an error message as an advisory on usage.
thanks so much,
Alan
aparcstats2table --hemi lh -s HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --parc BA --meas FoldInd --tablefile BA44 BA45 --subjectsfile=BA_LGI.txt
Usage: Converts a cortical stats file created by recon-all and or mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which each line is a subject and each column is a parcellation. By default, the values are the area of the parcellation in mm2. The first row is a list of the parcellation names. The first column is the subject name.
The subjects list can be specified on either of two ways: 1. Specify each subject after a -s flag
-s subject1 -s subject2 ... --hemi lh
2. Specify all subjects after --subjects flag. --subjects does not have to be the last argument. Eg:
--subjects subject1 subject2 ... --hemi lh
By default, it looks for the ?h.aparc.stats file based on the Killiany/Desikan parcellation atlas. This can be changed with '--parc parcellation' where parcellation is the parcellation to use. An alternative is aparc.a2009s which was developed by Christophe Destrieux. If this file is not found, it will exit with an error unless --skip in which case it skips this subject and moves on to the next.
By default, the area (mm2) of each parcellation is reported. This can be changed with '--meas measure', where measure can be area, volume (ie, volume of gray matter), thickness, thicknessstd, or meancurv. thicknessstd is the standard dev of thickness across space.
Example: aparcstats2table --hemi lh --subjects 004 008 --parc aparc.a2009s --meas meancurv -t lh.a2009s.meancurv.txt
lh.a2009s.meancurv.txt will have 3 rows: (1) 'header' with the name of each structure, (2) mean curvature for each structure for subject
The --common-parcs flag writes only the ROIs which are common to all the subjects. Default behavior is it puts 0.0 in the measure of an ROI which is not present in a subject.
The --parcs-from-file <file> outputs only the parcs specified in the file The order of the parcs in the file is maintained. Specify one parcellation per line.
The --report-rois flag, for each subject, gives what ROIs that are present in atleast one other subject is absent in current subject and also gives what ROIs are unique to the current subject.
The --transpose flag writes the transpose of the table. This might be a useful way to see the table when the number of subjects is relatively less than the number of ROIs.
The --delimiter option controls what character comes between the measures in the table. Valid options are 'tab' ( default), 'space', 'comma' and 'semicolon'.
The --skip option skips if it can't find a .stats file. Default behavior is exit the program.
The --parcid-only flag writes only the ROIs name in the 1st row 1st column of the table. Default is hemi_ROI_measure
On Tue, Sep 3, 2013 at 11:08 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Alan, it would be a lot easier to help if you told us what the error msg is:). Please supply the full terminal output including error msg. thanks doug
On 09/03/2013 10:52 AM, Alan Francis wrote:
Hi FreeSurfer folks:
I am trying to extract LGI values from Brodmann Areas 44 and 45. I am using the following script. Unfortunately it gives me an error message. Could you please help me.
aparcstats2table --skip -s /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --hemi lh --parc=BA --meas foldind --tablefile BA44 BA45 -lh.BA.stats --subjectsfile=BA_LGI.txt
thanks so much,
Alan Francis
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.
Your comamnd line is incorrect. Use --subjects instead of -s. Or just use only the --subjectsfile. doug
On 09/03/2013 11:55 AM, Alan Francis wrote:
Hi Doug:
Here is the message it gives. It's not so much an error message as an advisory on usage.
thanks so much,
Alan
aparcstats2table --hemi lh -s HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --parc BA --meas FoldInd --tablefile BA44 BA45 --subjectsfile=BA_LGI.txt
Usage: Converts a cortical stats file created by recon-all and or mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which each line is a subject and each column is a parcellation. By default, the values are the area of the parcellation in mm2. The first row is a list of the parcellation names. The first column is the subject name.
The subjects list can be specified on either of two ways:
Specify each subject after a -s flag
-s subject1 -s subject2 ... --hemi lhSpecify all subjects after --subjects flag. --subjects does not have to be the last argument. Eg:
--subjects subject1 subject2 ... --hemi lhBy default, it looks for the ?h.aparc.stats file based on the Killiany/Desikan parcellation atlas. This can be changed with '--parc parcellation' where parcellation is the parcellation to use. An alternative is aparc.a2009s which was developed by Christophe Destrieux. If this file is not found, it will exit with an error unless --skip in which case it skips this subject and moves on to the next.
By default, the area (mm2) of each parcellation is reported. This can be changed with '--meas measure', where measure can be area, volume (ie, volume of gray matter), thickness, thicknessstd, or meancurv. thicknessstd is the standard dev of thickness across space.
Example: aparcstats2table --hemi lh --subjects 004 008 --parc aparc.a2009s --meas meancurv -t lh.a2009s.meancurv.txt
lh.a2009s.meancurv.txt will have 3 rows: (1) 'header' with the name of each structure, (2) mean curvature for each structure for subject
The --common-parcs flag writes only the ROIs which are common to all the subjects. Default behavior is it puts 0.0 in the measure of an ROI which is not present in a subject.
The --parcs-from-file <file> outputs only the parcs specified in the file The order of the parcs in the file is maintained. Specify one parcellation per line.
The --report-rois flag, for each subject, gives what ROIs that are present in atleast one other subject is absent in current subject and also gives what ROIs are unique to the current subject.
The --transpose flag writes the transpose of the table. This might be a useful way to see the table when the number of subjects is relatively less than the number of ROIs.
The --delimiter option controls what character comes between the measures in the table. Valid options are 'tab' ( default), 'space', 'comma' and 'semicolon'.
The --skip option skips if it can't find a .stats file. Default behavior is exit the program.
The --parcid-only flag writes only the ROIs name in the 1st row 1st column of the table. Default is hemi_ROI_measure
On Tue, Sep 3, 2013 at 11:08 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Alan, it would be a lot easier to help if you told us what the error msg is:). Please supply the full terminal output including error msg. thanks doug On 09/03/2013 10:52 AM, Alan Francis wrote: > Hi FreeSurfer folks: > > I am trying to extract LGI values from Brodmann Areas 44 and 45. I am > using the following script. Unfortunately it gives me an error > message. Could you please help me. > > aparcstats2table --skip -s /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 > /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 > /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 > /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 > /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 > /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 > /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 > /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 > /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 > /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --hemi > lh --parc=BA --meas foldind --tablefile BA44 BA45 -lh.BA.stats > --subjectsfile=BA_LGI.txt > > > thanks so much, > > Alan Francis > > > _______________________________________________ > 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. 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.
Thanks Doug. So I change the command line syntax to the following:
csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] : aparcstats2table --hemi lh --subjects /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --parc BA --meas thickness --tablefile BA_LGI.txt
SUBJECTS_DIR : /media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF/ Parsing the .stats files ERROR: The stats file /HM0403/stats/lh.BA.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] :
When I use the -- skip flag it skips all the lh.BA.stats files. I am using FreeSurfer 5.0.
thanks so much,
Alan
On Tue, Sep 3, 2013 at 11:59 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Your comamnd line is incorrect. Use --subjects instead of -s. Or just use only the --subjectsfile. doug
On 09/03/2013 11:55 AM, Alan Francis wrote:
Hi Doug:
Here is the message it gives. It's not so much an error message as an advisory on usage.
thanks so much,
Alan
aparcstats2table --hemi lh -s HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --parc BA --meas FoldInd --tablefile BA44 BA45 --subjectsfile=BA_LGI.txt
Usage: Converts a cortical stats file created by recon-all and or mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which each line is a subject and each column is a parcellation. By default, the values are the area of the parcellation in mm2. The first row is a list of the parcellation names. The first column is the subject name.
The subjects list can be specified on either of two ways:
Specify each subject after a -s flag
-s subject1 -s subject2 ... --hemi lhSpecify all subjects after --subjects flag. --subjects does not have to be the last argument. Eg:
--subjects subject1 subject2 ... --hemi lhBy default, it looks for the ?h.aparc.stats file based on the Killiany/Desikan parcellation atlas. This can be changed with '--parc parcellation' where parcellation is the parcellation to use. An alternative is aparc.a2009s which was developed by Christophe Destrieux. If this file is not found, it will exit with an error unless --skip in which case it skips this subject and moves on to the next.
By default, the area (mm2) of each parcellation is reported. This can be changed with '--meas measure', where measure can be area, volume (ie, volume of gray matter), thickness, thicknessstd, or meancurv. thicknessstd is the standard dev of thickness across space.
Example: aparcstats2table --hemi lh --subjects 004 008 --parc aparc.a2009s --meas meancurv -t lh.a2009s.meancurv.txt
lh.a2009s.meancurv.txt will have 3 rows: (1) 'header' with the name of each structure, (2) mean curvature for each structure for subject
The --common-parcs flag writes only the ROIs which are common to all the subjects. Default behavior is it puts 0.0 in the measure of an ROI which is not present in a subject.
The --parcs-from-file <file> outputs only the parcs specified in the file The order of the parcs in the file is maintained. Specify one parcellation per line.
The --report-rois flag, for each subject, gives what ROIs that are present in atleast one other subject is absent in current subject and also gives what ROIs are unique to the current subject.
The --transpose flag writes the transpose of the table. This might be a useful way to see the table when the number of subjects is relatively less than the number of ROIs.
The --delimiter option controls what character comes between the measures in the table. Valid options are 'tab' ( default), 'space', 'comma' and 'semicolon'.
The --skip option skips if it can't find a .stats file. Default behavior is exit the program.
The --parcid-only flag writes only the ROIs name in the 1st row 1st column of the table. Default is hemi_ROI_measure
On Tue, Sep 3, 2013 at 11:08 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Hi Alan, it would be a lot easier to help if you told us what the error msg is:). Please supply the full terminal output including error msg. thanks doug On 09/03/2013 10:52 AM, Alan Francis wrote: > Hi FreeSurfer folks: > > I am trying to extract LGI values from Brodmann Areas 44 and 45. I am > using the following script. Unfortunately it gives me an error > message. Could you please help me. > > aparcstats2table --skip -s /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 > /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 > /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 > /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 > /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 > /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 > /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 > /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 > /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 > /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --hemi > lh --parc=BA --meas foldind --tablefile BA44 BA45 -lh.BA.stats > --subjectsfile=BA_LGI.txt > > > thanks so much, > > Alan Francis > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<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<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> <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> 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/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu 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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/
Hi Doug:
Maybe I did not communicate this effectively. Since the lh.BA.stats files are smaller in kb than the aparc files, I keep getting an error message when I run the aparcstats2table command which is as follows:
Parsing the .stats files ERROR: The stats file /HM0403/stats/lh.BA.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files csh::alanf@cerebro [/media/Alan_WORK/WORK/De_ LISI_Final/LGI_HSF] :
When I use the -- skip flag, it skips all the lh.BA.stats files. I am using FreeSurfer 5.0.
Could you please shed some light on this,
thanks so much,
Alan
On Tue, Sep 3, 2013 at 12:24 PM, Alan Francis alandarkenergy@gmail.comwrote:
Thanks Doug. So I change the command line syntax to the following:
csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] : aparcstats2table --hemi lh --subjects /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --parc BA --meas thickness --tablefile BA_LGI.txt
SUBJECTS_DIR : /media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF/ Parsing the .stats files ERROR: The stats file /HM0403/stats/lh.BA.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] :
When I use the -- skip flag it skips all the lh.BA.stats files. I am using FreeSurfer 5.0.
thanks so much,
Alan
On Tue, Sep 3, 2013 at 11:59 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Your comamnd line is incorrect. Use --subjects instead of -s. Or just use only the --subjectsfile. doug
On 09/03/2013 11:55 AM, Alan Francis wrote:
Hi Doug:
Here is the message it gives. It's not so much an error message as an advisory on usage.
thanks so much,
Alan
aparcstats2table --hemi lh -s HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --parc BA --meas FoldInd --tablefile BA44 BA45 --subjectsfile=BA_LGI.txt
Usage: Converts a cortical stats file created by recon-all and or mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which each line is a subject and each column is a parcellation. By default, the values are the area of the parcellation in mm2. The first row is a list of the parcellation names. The first column is the subject name.
The subjects list can be specified on either of two ways:
Specify each subject after a -s flag
-s subject1 -s subject2 ... --hemi lhSpecify all subjects after --subjects flag. --subjects does not have to be the last argument. Eg:
--subjects subject1 subject2 ... --hemi lhBy default, it looks for the ?h.aparc.stats file based on the Killiany/Desikan parcellation atlas. This can be changed with '--parc parcellation' where parcellation is the parcellation to use. An alternative is aparc.a2009s which was developed by Christophe Destrieux. If this file is not found, it will exit with an error unless --skip in which case it skips this subject and moves on to the next.
By default, the area (mm2) of each parcellation is reported. This can be changed with '--meas measure', where measure can be area, volume (ie, volume of gray matter), thickness, thicknessstd, or meancurv. thicknessstd is the standard dev of thickness across space.
Example: aparcstats2table --hemi lh --subjects 004 008 --parc aparc.a2009s --meas meancurv -t lh.a2009s.meancurv.txt
lh.a2009s.meancurv.txt will have 3 rows: (1) 'header' with the name of each structure, (2) mean curvature for each structure for subject
The --common-parcs flag writes only the ROIs which are common to all the subjects. Default behavior is it puts 0.0 in the measure of an ROI which is not present in a subject.
The --parcs-from-file <file> outputs only the parcs specified in the file The order of the parcs in the file is maintained. Specify one parcellation per line.
The --report-rois flag, for each subject, gives what ROIs that are present in atleast one other subject is absent in current subject and also gives what ROIs are unique to the current subject.
The --transpose flag writes the transpose of the table. This might be a useful way to see the table when the number of subjects is relatively less than the number of ROIs.
The --delimiter option controls what character comes between the measures in the table. Valid options are 'tab' ( default), 'space', 'comma' and 'semicolon'.
The --skip option skips if it can't find a .stats file. Default behavior is exit the program.
The --parcid-only flag writes only the ROIs name in the 1st row 1st column of the table. Default is hemi_ROI_measure
On Tue, Sep 3, 2013 at 11:08 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Hi Alan, it would be a lot easier to help if you told us what the error msg is:). Please supply the full terminal output including error msg. thanks doug On 09/03/2013 10:52 AM, Alan Francis wrote: > Hi FreeSurfer folks: > > I am trying to extract LGI values from Brodmann Areas 44 and 45. I am > using the following script. Unfortunately it gives me an error > message. Could you please help me. > > aparcstats2table --skip -s /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 > /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 > /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 > /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 > /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 > /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 > /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 > /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 > /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 > /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --hemi > lh --parc=BA --meas foldind --tablefile BA44 BA45 -lh.BA.stats > --subjectsfile=BA_LGI.txt > > > thanks so much, > > Alan Francis > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<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<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> <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> 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/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu 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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/
Hi Doug:
I solved the problem. The aparcstats2table script works. But I have another. It appears that the script does not recognize "foldind" or FoldInd, so how do I get LGI values of the Brodmann areas?
thank you,
Alan
On Tue, Sep 3, 2013 at 1:30 PM, Alan Francis alandarkenergy@gmail.comwrote:
Hi Doug:
Maybe I did not communicate this effectively. Since the lh.BA.stats files are smaller in kb than the aparc files, I keep getting an error message when I run the aparcstats2table command which is as follows:
Parsing the .stats files ERROR: The stats file /HM0403/stats/lh.BA.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files csh::alanf@cerebro [/media/Alan_WORK/WORK/De_ LISI_Final/LGI_HSF] :
When I use the -- skip flag, it skips all the lh.BA.stats files. I am using FreeSurfer 5.0.
Could you please shed some light on this,
thanks so much,
Alan
On Tue, Sep 3, 2013 at 12:24 PM, Alan Francis alandarkenergy@gmail.comwrote:
Thanks Doug. So I change the command line syntax to the following:
csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] : aparcstats2table --hemi lh --subjects /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --parc BA --meas thickness --tablefile BA_LGI.txt
SUBJECTS_DIR : /media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF/ Parsing the .stats files ERROR: The stats file /HM0403/stats/lh.BA.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files csh::alanf@cerebro [/media/Alan_WORK/WORK/De_LISI_Final/LGI_HSF] :
When I use the -- skip flag it skips all the lh.BA.stats files. I am using FreeSurfer 5.0.
thanks so much,
Alan
On Tue, Sep 3, 2013 at 11:59 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Your comamnd line is incorrect. Use --subjects instead of -s. Or just use only the --subjectsfile. doug
On 09/03/2013 11:55 AM, Alan Francis wrote:
Hi Doug:
Here is the message it gives. It's not so much an error message as an advisory on usage.
thanks so much,
Alan
aparcstats2table --hemi lh -s HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --parc BA --meas FoldInd --tablefile BA44 BA45 --subjectsfile=BA_LGI.txt
Usage: Converts a cortical stats file created by recon-all and or mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which each line is a subject and each column is a parcellation. By default, the values are the area of the parcellation in mm2. The first row is a list of the parcellation names. The first column is the subject name.
The subjects list can be specified on either of two ways:
Specify each subject after a -s flag
-s subject1 -s subject2 ... --hemi lhSpecify all subjects after --subjects flag. --subjects does not
have to be the last argument. Eg:
--subjects subject1 subject2 ... --hemi lhBy default, it looks for the ?h.aparc.stats file based on the Killiany/Desikan parcellation atlas. This can be changed with '--parc parcellation' where parcellation is the parcellation to use. An alternative is aparc.a2009s which was developed by Christophe Destrieux. If this file is not found, it will exit with an error unless --skip in which case it skips this subject and moves on to the next.
By default, the area (mm2) of each parcellation is reported. This can be changed with '--meas measure', where measure can be area, volume (ie, volume of gray matter), thickness, thicknessstd, or meancurv. thicknessstd is the standard dev of thickness across space.
Example: aparcstats2table --hemi lh --subjects 004 008 --parc aparc.a2009s --meas meancurv -t lh.a2009s.meancurv.txt
lh.a2009s.meancurv.txt will have 3 rows: (1) 'header' with the name of each structure, (2) mean curvature for each structure for subject
The --common-parcs flag writes only the ROIs which are common to all the subjects. Default behavior is it puts 0.0 in the measure of an ROI which is not present in a subject.
The --parcs-from-file <file> outputs only the parcs specified in the file The order of the parcs in the file is maintained. Specify one parcellation per line.
The --report-rois flag, for each subject, gives what ROIs that are present in atleast one other subject is absent in current subject and also gives what ROIs are unique to the current subject.
The --transpose flag writes the transpose of the table. This might be a useful way to see the table when the number of subjects is relatively less than the number of ROIs.
The --delimiter option controls what character comes between the measures in the table. Valid options are 'tab' ( default), 'space', 'comma' and 'semicolon'.
The --skip option skips if it can't find a .stats file. Default behavior is exit the program.
The --parcid-only flag writes only the ROIs name in the 1st row 1st column of the table. Default is hemi_ROI_measure
On Tue, Sep 3, 2013 at 11:08 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Hi Alan, it would be a lot easier to help if you told us what the error msg is:). Please supply the full terminal output including errormsg. thanks doug
On 09/03/2013 10:52 AM, Alan Francis wrote: > Hi FreeSurfer folks: > > I am trying to extract LGI values from Brodmann Areas 44 and 45. I am > using the following script. Unfortunately it gives me an error > message. Could you please help me. > > aparcstats2table --skip -s /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 > /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 > /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 > /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 > /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 > /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 > /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 > /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 > /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 > /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --hemi > lh --parc=BA --meas foldind --tablefile BA44 BA45 -lh.BA.stats > --subjectsfile=BA_LGI.txt > > > thanks so much, > > Alan Francis > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<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<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> <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> 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/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu 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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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@nmr.mgh.harvard.edu
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Alan Francis -
Douglas N Greve