Dear list,
I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using :
mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
(Please let me know if this is not correct)
I then get this output ( for each individual)
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7953 5220.0 Seg0000 2.4055 0.4052 1.5796 2.9763 1.3967 2 1 156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977
I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal?
Thank you very much
Anna
that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1
doug
On 11/13/2013 11:45 AM, Anna Jonsson wrote:
Dear list,
I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using :
mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
(Please let me know if this is not correct)
I then get this output ( for each individual)
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7953 5220.0 Seg0000 2.4055 0.4052 1.5796 2.9763 1.3967
2 1 156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977
I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal?
Thank you very much
Anna
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units?
Thanks again
On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1
doug
On 11/13/2013 11:45 AM, Anna Jonsson wrote:
Dear list,
I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using :
mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i
$SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
(Please let me know if this is not correct)
I then get this output ( for each individual)
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min
Max Range
1 0 7953 5220.0 Seg0000 2.4055 0.4052 1.5796
2.9763 1.39672 1 156737 101379.9 Seg0001 2.9472 0.9038 1.7030
6.0007 4.2977I assume one of these values (if above command has worked correctly)
contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal?
Thank you very much
Anna
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.
yes and yes
On 11/13/2013 12:04 PM, Anna Jonsson wrote:
Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units?
Thanks again
On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1 doug On 11/13/2013 11:45 AM, Anna Jonsson wrote: > Dear list, > > I have a question about extracting global lgi values/hemisphere. I > think I have managed to do it correctly using : > > mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats > > (Please let me know if this is not correct) > > > I then get this output ( for each individual) > > ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range > 1 0 7953 5220.0 Seg0000 2.4055 0.4052 1.5796 2.9763 1.3967 > > 2 1 156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 > > I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? > > > Thank you very much > > Anna > > > _______________________________________________ > 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.
Thank you. Can I then use
aparcstats2table --subjects XXXX --hemi lh --meas thickness --parc lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in 1 tablefile or should I use other command?
On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
yes and yes
On 11/13/2013 12:04 PM, Anna Jonsson wrote:
Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units?
Thanks again
On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1 doug On 11/13/2013 11:45 AM, Anna Jonsson wrote: > Dear list, > > I have a question about extracting global lgi values/hemisphere. I > think I have managed to do it correctly using : > > mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats > > (Please let me know if this is not correct) > > > I then get this output ( for each individual) > > ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range > 1 0 7953 5220.0 Seg0000 2.4055 0.40521.5796 2.9763 1.3967 > > 2 1 156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 > > I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? > > > Thank you very much > > Anna > > > _______________________________________________ > 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.eduhttps://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.-- 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/
I think it would be
--parc aparc.pial_lgi
doug
On 11/14/2013 11:27 AM, Anna Jonsson wrote:
Thank you. Can I then use aparcstats2table --subjects XXXX --hemi lh --meas thickness --parc lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in 1 tablefile or should I use other command?
On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
yes and yes On 11/13/2013 12:04 PM, Anna Jonsson wrote: Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units? Thanks again On Wed, Nov 13, 2013 at 4:56 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: that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1 doug On 11/13/2013 11:45 AM, Anna Jonsson wrote: > Dear list, > > I have a question about extracting global lgi values/hemisphere. I > think I have managed to do it correctly using : > > mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats > > (Please let me know if this is not correct) > > > I then get this output ( for each individual) > > ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range > 1 0 7953 5220.0 Seg0000 2.4055 0.4052 <tel:2.4055%20%20%200.4052> 1.5796 2.9763 1.3967 > > 2 1 156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 > > I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? > > > Thank you very much > > Anna > > > _______________________________________________ > 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. -- 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/
Thank you. I have tried to write a script to make this above process automatic but it doesn't work. Any tips on how to make the above process into a script for a number of subjects ?
Kind Wishes,
Anna
On Thu, Nov 14, 2013 at 7:39 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
I think it would be
--parc aparc.pial_lgi
doug
On 11/14/2013 11:27 AM, Anna Jonsson wrote:
Thank you. Can I then use aparcstats2table --subjects XXXX --hemi lh --meas thickness --parc lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in 1 tablefile or should I use other command?
On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
yes and yes On 11/13/2013 12:04 PM, Anna Jonsson wrote: Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units? Thanks again On Wed, Nov 13, 2013 at 4:56 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: that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1 doug On 11/13/2013 11:45 AM, Anna Jonsson wrote: > Dear list, > > I have a question about extracting global lgi values/hemisphere. I > think I have managed to do it correctly using : > > mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats > > (Please let me know if this is not correct) > > > I then get this output ( for each individual) > > ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range > 1 0 7953 5220.0 Seg0000 2.4055 0.4052 <tel:2.4055%20%20%200.4052> 1.5796 2.9763 1.3967 > > 2 1 156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 > > I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? > > > Thank you very much > > Anna > > > _______________________________________________ > 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 sentto 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 <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/-- 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/
Which "above process" do you mean?
On 11/17/2013 04:57 AM, Anna Jonsson wrote:
Thank you. I have tried to write a script to make this above process automatic but it doesn't work. Any tips on how to make the above process into a script for a number of subjects ?
Kind Wishes,
Anna
On Thu, Nov 14, 2013 at 7:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think it would be --parc aparc.pial_lgi doug On 11/14/2013 11:27 AM, Anna Jonsson wrote: Thank you. Can I then use aparcstats2table --subjects XXXX --hemi lh --meas thickness --parc lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in 1 tablefile or should I use other command? On Wed, Nov 13, 2013 at 6:59 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: yes and yes On 11/13/2013 12:04 PM, Anna Jonsson wrote: Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units? Thanks again On Wed, Nov 13, 2013 at 4:56 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: that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1 doug On 11/13/2013 11:45 AM, Anna Jonsson wrote: > Dear list, > > I have a question about extracting global lgi values/hemisphere. I > think I have managed to do it correctly using : > > mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats > > (Please let me know if this is not correct) > > > I then get this output ( for each individual) > > ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range > 1 0 7953 5220.0 Seg0000 2.4055 0.4052 <tel:2.4055%20%20%200.4052> 1.5796 2.9763 1.3967 > > 2 1 156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 > > I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? > > > Thank you very much > > Anna > > > _______________________________________________ > 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. -- 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/ -- 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@nmr.mgh.harvard.edu
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Anna Jonsson -
Douglas N Greve