All,
I am going to run an analysis of cortical thickness reproducibility; there are at least two methods that seem obvious. I could run qdec analysis with time1 and time2 as different groups or I could run the methods below. Are the commands below the same ones used in the qdec GUI? As far as I can tell, they will both give me cortical thickness differences on a vertex by vertex basis. There are probably some subtle differences in the way they are coded, but any major changes? Thanks.
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
The two methods are very different. In the method described on the thickness repeatability page, its computing a mean and stddev of the thickness for your group. This a direct and easily interpretable measure, but doesn't give you a statistical measure (but you could do that on your own with some external package).
In qdec (mri_glmfit), it would be conducting a GLM-based analysis looking for statistical significance, expressed as a p-value at each vertex, in thickness between groups. Here, raw thickness differences are hidden in the analysis.
However, you can of course do both analysis, and compare them, which I would suggest you do. You would hope the areas of change are the same. Note that you can load external surface maps, such as a thickness- diff.mgh map, onto the fsaverage surface in qdec, so that you can view both analysis (or just load the thickness-diff.mgh map in tksurfer).
Its on the list of things to add to qdec to create two-group thickness difference maps, as well as just viewing the mean group thickness, to save some work for this sort of thing.
Nick
On Fri, 2009-02-20 at 12:53 -0600, bell0368@umn.edu wrote:
All,
I am going to run an analysis of cortical thickness reproducibility; there are at least two methods that seem obvious. I could run qdec analysis with time1 and time2 as different groups or I could run the methods below. Are the commands below the same ones used in the qdec GUI? As far as I can tell, they will both give me cortical thickness differences on a vertex by vertex basis. There are probably some subtle differences in the way they are coded, but any major changes? Thanks.
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You could extend the analysis described on that wiki page by calculating tstats and pvalues (in addition to mean and stdev). Then you have a paired t-test, whereas mri_glmfit with qdec would be doing an unpaired t-test. I think preproc has an option to calculate within subject differences for a paired t-test with mri_glmfit as well. As you may know, paired t-tests are more sensitive than unpaired t-tests, and are generally more appropriate when you make within subject comparisons. On the other hand, if you intend your exercise to be a test for the likelihood of false positive differences between groups, the unpaired t-test may be more appropriate.
Subject: Re: [Freesurfer] qdec thickness and repeatability From: nicks@nmr.mgh.harvard.edu To: bell0368@umn.edu Date: Fri, 20 Feb 2009 15:15:10 -0500 CC: freesurfer@nmr.mgh.harvard.edu
The two methods are very different. In the method described on the thickness repeatability page, its computing a mean and stddev of the thickness for your group. This a direct and easily interpretable measure, but doesn't give you a statistical measure (but you could do that on your own with some external package).
In qdec (mri_glmfit), it would be conducting a GLM-based analysis looking for statistical significance, expressed as a p-value at each vertex, in thickness between groups. Here, raw thickness differences are hidden in the analysis.
However, you can of course do both analysis, and compare them, which I would suggest you do. You would hope the areas of change are the same. Note that you can load external surface maps, such as a thickness- diff.mgh map, onto the fsaverage surface in qdec, so that you can view both analysis (or just load the thickness-diff.mgh map in tksurfer).
Its on the list of things to add to qdec to create two-group thickness difference maps, as well as just viewing the mean group thickness, to save some work for this sort of thing.
Nick
On Fri, 2009-02-20 at 12:53 -0600, bell0368@umn.edu wrote:
All,
I am going to run an analysis of cortical thickness reproducibility; there are at least two methods that seem obvious. I could run qdec analysis with time1 and time2 as different groups or I could run the methods below. Are the commands below the same ones used in the qdec GUI? As far as I can tell, they will both give me cortical thickness differences on a vertex by vertex basis. There are probably some subtle differences in the way they are coded, but any major changes? Thanks.
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
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
_________________________________________________________________ Windows Live™ Hotmail®:…more than just e-mail. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_explore...
Info on doing the paired t is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
Don Hagler wrote:
You could extend the analysis described on that wiki page by calculating tstats and pvalues (in addition to mean and stdev). Then you have a paired t-test, whereas mri_glmfit with qdec would be doing an unpaired t-test. I think preproc has an option to calculate within subject differences for a paired t-test with mri_glmfit as well. As you may know, paired t-tests are more sensitive than unpaired t-tests, and are generally more appropriate when you make within subject comparisons. On the other hand, if you intend your exercise to be a test for the likelihood of false positive differences between groups, the unpaired t-test may be more appropriate.
Subject: Re: [Freesurfer] qdec thickness and repeatability From: nicks@nmr.mgh.harvard.edu To: bell0368@umn.edu Date: Fri, 20 Feb 2009 15:15:10 -0500 CC: freesurfer@nmr.mgh.harvard.edu
The two methods are very different. In the method described on the thickness repeatability page, its computing a mean and stddev of the thickness for your group. This a direct and easily interpretable measure, but doesn't give you a statistical measure (but you could do that on your own with some external package).
In qdec (mri_glmfit), it would be conducting a GLM-based analysis looking for statistical significance, expressed as a p-value at each vertex, in thickness between groups. Here, raw thickness differences are hidden in the analysis.
However, you can of course do both analysis, and compare them, which I would suggest you do. You would hope the areas of change are the same. Note that you can load external surface maps, such as a thickness- diff.mgh map, onto the fsaverage surface in qdec, so that you can view both analysis (or just load the thickness-diff.mgh map in tksurfer).
Its on the list of things to add to qdec to create two-group thickness difference maps, as well as just viewing the mean group thickness, to save some work for this sort of thing.
Nick
On Fri, 2009-02-20 at 12:53 -0600, bell0368@umn.edu wrote:
All,
I am going to run an analysis of cortical thickness
reproducibility; there
are at least two methods that seem obvious. I could run qdec
analysis with
time1 and time2 as different groups or I could run the methods
below. Are
the commands below the same ones used in the qdec GUI? As far as I
can
tell, they will both give me cortical thickness differences on a
vertex by
vertex basis. There are probably some subtle differences in the
way they
are coded, but any major changes? Thanks.
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
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
Windows Live™ Hotmail®:…more than just e-mail. Check it out. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_explore_022009
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the info. I am getting an error on the mri_surf2surf step of the thickdiffmap.sh script. It occurs whether I use subj1, subj2, fsaverage, or a different person (subj3) in the command below. There was one comment from Bruce in the archives that says this error will occur if the registration is poor. The inter-subject, i.e. subj1_to_subj2, registration is fine, as shown with tkregister2. I am not sure how to quality/error check the registration to the sphere. On a more general note, this step is supposed to resample the cortical difference map to the template subject (--trgsubject), I guess I am a bit unclear as to why sphere.reg is needed, considering that my --trgsubject could be anything, not necessary the standard sphere. Does mri_surf2surf first align the subj1 standard sphere vertices to the --trgsubject and then align the difference map using the same transform? Thanks for any help.
thickdiffmap.sh 1633_20170_1271 1633_20240_1280 fsaverage lh 1 2 3 | tee > output5.log
mri_surf2surf --srcsubject 1633_20170_1271 --sval /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271 /surf/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh --trgsubject fsaverage --tval /home/bfs-raid3/chris/18 2_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20170_1271_to_1633_20240_1280_resampled _to_fsaverage.mgh --hemi lh --surfreg sphere.reg Registration surface changed to sphere.reg srcsubject = 1633_20170_1271 srcval = /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.thickness_diff_1633_20170_12 71_to_1633_20240_1280.mgh srctype = trgsubject = fsaverage trgval = /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20 170_1271_to_1633_20240_1280_resampled_to_fsaverage.mgh trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.sphere.reg Loading source data Segmentation fault (above is in my log file) (below is error printed to the screen) INFO:try to get src info from transform. MRIalloc(1879048192, -1125858646, 317): bad parm Cannot allocate memory
On Feb 23 2009, Douglas N Greve wrote:
Info on doing the paired t is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
Don Hagler wrote:
You could extend the analysis described on that wiki page by calculating tstats and pvalues (in addition to mean and stdev). Then you have a paired t-test, whereas mri_glmfit with qdec would be doing an unpaired t-test. I think preproc has an option to calculate within subject differences for a paired t-test with mri_glmfit as well. As you may know, paired t-tests are more sensitive than unpaired t-tests, and are generally more appropriate when you make within subject comparisons. On the other hand, if you intend your exercise to be a test for the likelihood of false positive differences between groups, the unpaired t-test may be more appropriate.
Subject: Re: [Freesurfer] qdec thickness and repeatability From: nicks@nmr.mgh.harvard.edu To: bell0368@umn.edu Date: Fri, 20 Feb 2009 15:15:10 -0500 CC: freesurfer@nmr.mgh.harvard.edu
The two methods are very different. In the method described on the thickness repeatability page, its computing a mean and stddev of the thickness for your group. This a direct and easily interpretable measure, but doesn't give you a statistical measure (but you could do that on your own with some external package).
In qdec (mri_glmfit), it would be conducting a GLM-based analysis looking for statistical significance, expressed as a p-value at each vertex, in thickness between groups. Here, raw thickness differences are hidden in the analysis.
However, you can of course do both analysis, and compare them, which I would suggest you do. You would hope the areas of change are the same. Note that you can load external surface maps, such as a thickness- diff.mgh map, onto the fsaverage surface in qdec, so that you can view both analysis (or just load the thickness-diff.mgh map in tksurfer).
Its on the list of things to add to qdec to create two-group thickness difference maps, as well as just viewing the mean group thickness, to save some work for this sort of thing.
Nick
On Fri, 2009-02-20 at 12:53 -0600, bell0368@umn.edu wrote:
All,
I am going to run an analysis of cortical thickness
reproducibility; there
are at least two methods that seem obvious. I could run qdec
analysis with
time1 and time2 as different groups or I could run the methods
below. Are
the commands below the same ones used in the qdec GUI? As far as I
can
tell, they will both give me cortical thickness differences on a
vertex by
vertex basis. There are probably some subtle differences in the
way they
are coded, but any major changes? Thanks.
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
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
Windows Live Hotmail®: more than just e-mail. Check it out. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_explore_022009
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what do you get if you run mri_info on the sval file?
bell0368@umn.edu wrote:
Thanks for the info. I am getting an error on the mri_surf2surf step of the thickdiffmap.sh script. It occurs whether I use subj1, subj2, fsaverage, or a different person (subj3) in the command below. There was one comment from Bruce in the archives that says this error will occur if the registration is poor. The inter-subject, i.e. subj1_to_subj2, registration is fine, as shown with tkregister2. I am not sure how to quality/error check the registration to the sphere. On a more general note, this step is supposed to resample the cortical difference map to the template subject (--trgsubject), I guess I am a bit unclear as to why sphere.reg is needed, considering that my --trgsubject could be anything, not necessary the standard sphere. Does mri_surf2surf first align the subj1 standard sphere vertices to the --trgsubject and then align the difference map using the same transform? Thanks for any help.
thickdiffmap.sh 1633_20170_1271 1633_20240_1280 fsaverage lh 1 2 3 | tee > output5.log
mri_surf2surf --srcsubject 1633_20170_1271 --sval /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271 /surf/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh --trgsubject fsaverage --tval /home/bfs-raid3/chris/18 2_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20170_1271_to_1633_20240_1280_resampled _to_fsaverage.mgh --hemi lh --surfreg sphere.reg Registration surface changed to sphere.reg srcsubject = 1633_20170_1271 srcval = /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.thickness_diff_1633_20170_12
71_to_1633_20240_1280.mgh srctype = trgsubject = fsaverage trgval = /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20
170_1271_to_1633_20240_1280_resampled_to_fsaverage.mgh trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.sphere.reg Loading source data Segmentation fault (above is in my log file) (below is error printed to the screen) INFO:try to get src info from transform. MRIalloc(1879048192, -1125858646, 317): bad parm Cannot allocate memory
On Feb 23 2009, Douglas N Greve wrote:
Info on doing the paired t is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
Don Hagler wrote:
You could extend the analysis described on that wiki page by calculating tstats and pvalues (in addition to mean and stdev). Then you have a paired t-test, whereas mri_glmfit with qdec would be doing an unpaired t-test. I think preproc has an option to calculate within subject differences for a paired t-test with mri_glmfit as well. As you may know, paired t-tests are more sensitive than unpaired t-tests, and are generally more appropriate when you make within subject comparisons. On the other hand, if you intend your exercise to be a test for the likelihood of false positive differences between groups, the unpaired t-test may be more appropriate.
Subject: Re: [Freesurfer] qdec thickness and repeatability From: nicks@nmr.mgh.harvard.edu To: bell0368@umn.edu Date: Fri, 20 Feb 2009 15:15:10 -0500 CC: freesurfer@nmr.mgh.harvard.edu
The two methods are very different. In the method described on the thickness repeatability page, its computing a mean and stddev of the thickness for your group. This a direct and easily interpretable measure, but doesn't give you a statistical measure (but you could do that on your own with some external package).
In qdec (mri_glmfit), it would be conducting a GLM-based analysis looking for statistical significance, expressed as a p-value at each vertex, in thickness between groups. Here, raw thickness differences are hidden in the analysis.
However, you can of course do both analysis, and compare them,
which I
would suggest you do. You would hope the areas of change are the
same.
Note that you can load external surface maps, such as a thickness- diff.mgh map, onto the fsaverage surface in qdec, so that you can
view
both analysis (or just load the thickness-diff.mgh map in tksurfer).
Its on the list of things to add to qdec to create two-group
thickness
difference maps, as well as just viewing the mean group thickness, to save some work for this sort of thing.
Nick
On Fri, 2009-02-20 at 12:53 -0600, bell0368@umn.edu wrote:
All,
I am going to run an analysis of cortical thickness
reproducibility; there
are at least two methods that seem obvious. I could run qdec
analysis with
time1 and time2 as different groups or I could run the methods
below. Are
the commands below the same ones used in the qdec GUI? As far as
I can
tell, they will both give me cortical thickness differences on a
vertex by
vertex basis. There are probably some subtle differences in the
way they
are coded, but any major changes? Thanks.
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
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
Windows Live™ Hotmail®:…more than just e-mail. Check it out. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_explore_022009
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
what version of freesurfer is being used?
type 'freesurfer --version' and its the last line.
On Mon, 2009-02-23 at 14:08 -0600, bell0368@umn.edu wrote:
Thanks for the info. I am getting an error on the mri_surf2surf step of the thickdiffmap.sh script. It occurs whether I use subj1, subj2, fsaverage, or a different person (subj3) in the command below. There was one comment from Bruce in the archives that says this error will occur if the registration is poor. The inter-subject, i.e. subj1_to_subj2, registration is fine, as shown with tkregister2. I am not sure how to quality/error check the registration to the sphere. On a more general note, this step is supposed to resample the cortical difference map to the template subject (--trgsubject), I guess I am a bit unclear as to why sphere.reg is needed, considering that my --trgsubject could be anything, not necessary the standard sphere. Does mri_surf2surf first align the subj1 standard sphere vertices to the --trgsubject and then align the difference map using the same transform? Thanks for any help.
thickdiffmap.sh 1633_20170_1271 1633_20240_1280 fsaverage lh 1 2 3 | tee > output5.log
mri_surf2surf --srcsubject 1633_20170_1271 --sval /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271 /surf/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh --trgsubject fsaverage --tval /home/bfs-raid3/chris/18 2_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20170_1271_to_1633_20240_1280_resampled _to_fsaverage.mgh --hemi lh --surfreg sphere.reg Registration surface changed to sphere.reg srcsubject = 1633_20170_1271 srcval = /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.thickness_diff_1633_20170_12 71_to_1633_20240_1280.mgh srctype = trgsubject = fsaverage trgval = /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20 170_1271_to_1633_20240_1280_resampled_to_fsaverage.mgh trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.sphere.reg Loading source data Segmentation fault (above is in my log file) (below is error printed to the screen) INFO:try to get src info from transform. MRIalloc(1879048192, -1125858646, 317): bad parm Cannot allocate memory
On Feb 23 2009, Douglas N Greve wrote:
Info on doing the paired t is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
Don Hagler wrote:
You could extend the analysis described on that wiki page by calculating tstats and pvalues (in addition to mean and stdev). Then you have a paired t-test, whereas mri_glmfit with qdec would be doing an unpaired t-test. I think preproc has an option to calculate within subject differences for a paired t-test with mri_glmfit as well. As you may know, paired t-tests are more sensitive than unpaired t-tests, and are generally more appropriate when you make within subject comparisons. On the other hand, if you intend your exercise to be a test for the likelihood of false positive differences between groups, the unpaired t-test may be more appropriate.
Subject: Re: [Freesurfer] qdec thickness and repeatability From: nicks@nmr.mgh.harvard.edu To: bell0368@umn.edu Date: Fri, 20 Feb 2009 15:15:10 -0500 CC: freesurfer@nmr.mgh.harvard.edu
The two methods are very different. In the method described on the thickness repeatability page, its computing a mean and stddev of the thickness for your group. This a direct and easily interpretable measure, but doesn't give you a statistical measure (but you could do that on your own with some external package).
In qdec (mri_glmfit), it would be conducting a GLM-based analysis looking for statistical significance, expressed as a p-value at each vertex, in thickness between groups. Here, raw thickness differences are hidden in the analysis.
However, you can of course do both analysis, and compare them, which I would suggest you do. You would hope the areas of change are the same. Note that you can load external surface maps, such as a thickness- diff.mgh map, onto the fsaverage surface in qdec, so that you can view both analysis (or just load the thickness-diff.mgh map in tksurfer).
Its on the list of things to add to qdec to create two-group thickness difference maps, as well as just viewing the mean group thickness, to save some work for this sort of thing.
Nick
On Fri, 2009-02-20 at 12:53 -0600, bell0368@umn.edu wrote:
All,
I am going to run an analysis of cortical thickness
reproducibility; there
are at least two methods that seem obvious. I could run qdec
analysis with
time1 and time2 as different groups or I could run the methods
below. Are
the commands below the same ones used in the qdec GUI? As far as I
can
tell, they will both give me cortical thickness differences on a
vertex by
vertex basis. There are probably some subtle differences in the
way they
are coded, but any major changes? Thanks.
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
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
Windows Live™ Hotmail®:…more than just e-mail. Check it out. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_explore_022009
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
The machine I am running on has 14 GB of memory, is there a limit on the size mri_info will read? Also, from "du" it appears to only take up 1.1M. I am running Freesurfer 4.0 on Centos4.
mri_info 1633_20170_1271/surf/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh TAGskip: failed to calloc 3623878656 bytes!
Cannot allocate memory //////
du -sch 1633_20170_1271/surf/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh
1.1M 1633_20170_1271/sur/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh
1.1M total
On Feb 23 2009, Nick Schmansky wrote:
what version of freesurfer is being used?
type 'freesurfer --version' and its the last line.
On Mon, 2009-02-23 at 14:08 -0600, bell0368@umn.edu wrote:
Thanks for the info. I am getting an error on the mri_surf2surf step of the thickdiffmap.sh script. It occurs whether I use subj1, subj2, fsaverage, or a different person (subj3) in the command below. There was one comment from Bruce in the archives that says this error will occur if the registration is poor. The inter-subject, i.e. subj1_to_subj2, registration is fine, as shown with tkregister2. I am not sure how to quality/error check the registration to the sphere. On a more general note, this step is supposed to resample the cortical difference map to the template subject (--trgsubject), I guess I am a bit unclear as to why sphere.reg is needed, considering that my --trgsubject could be anything, not necessary the standard sphere. Does mri_surf2surf first align the subj1 standard sphere vertices to the --trgsubject and then align the difference map using the same transform? Thanks for any help.
thickdiffmap.sh 1633_20170_1271 1633_20240_1280 fsaverage lh 1 2 3 | tee > output5.log
mri_surf2surf --srcsubject 1633_20170_1271 --sval /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271 /surf/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh --trgsubject fsaverage --tval /home/bfs-raid3/chris/18
2_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20170_1271_to_1633_20240_1280_resampled _to_fsaverage.mgh --hemi lh --surfreg sphere.reg Registration surface changed to sphere.reg srcsubject = 1633_20170_1271 srcval = /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.thickness_diff_1633_20170_12 71_to_1633_20240_1280.mgh srctype = trgsubject = fsaverage trgval = /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20 170_1271_to_1633_20240_1280_resampled_to_fsaverage.mgh trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.sphere.reg Loading source data Segmentation fault (above is in my log file) (below is error printed to the screen) INFO:try to get src info from transform. MRIalloc(1879048192, -1125858646, 317): bad parm Cannot allocate memory
On Feb 23 2009, Douglas N Greve wrote:
Info on doing the paired t is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
Don Hagler wrote:
You could extend the analysis described on that wiki page by calculating tstats and pvalues (in addition to mean and stdev). Then you have a paired t-test, whereas mri_glmfit with qdec would be doing an unpaired t-test. I think preproc has an option to calculate within subject differences for a paired t-test with mri_glmfit as well. As you may know, paired t-tests are more sensitive than unpaired t-tests, and are generally more appropriate when you make within subject comparisons. On the other hand, if you intend your exercise to be a test for the likelihood of false positive differences between groups, the unpaired t-test may be more appropriate.
Subject: Re: [Freesurfer] qdec thickness and repeatability From: nicks@nmr.mgh.harvard.edu To: bell0368@umn.edu Date: Fri, 20 Feb 2009 15:15:10 -0500 CC: freesurfer@nmr.mgh.harvard.edu
The two methods are very different. In the method described on the thickness repeatability page, its computing a mean and stddev of the thickness for your group. This a direct and easily interpretable measure, but doesn't give you a statistical measure (but you could do that on your own with some external package).
In qdec (mri_glmfit), it would be conducting a GLM-based analysis looking for statistical significance, expressed as a p-value at each vertex, in thickness between groups. Here, raw thickness differences are hidden in the analysis.
However, you can of course do both analysis, and compare them, which I would suggest you do. You would hope the areas of change are the same. Note that you can load external surface maps, such as a thickness- diff.mgh map, onto the fsaverage surface in qdec, so that you can view both analysis (or just load the thickness-diff.mgh map in tksurfer).
Its on the list of things to add to qdec to create two-group thickness difference maps, as well as just viewing the mean group thickness, to save some work for this sort of thing.
Nick
On Fri, 2009-02-20 at 12:53 -0600, bell0368@umn.edu wrote:
All,
I am going to run an analysis of cortical thickness
reproducibility; there
are at least two methods that seem obvious. I could run qdec
analysis with
time1 and time2 as different groups or I could run the methods
below. Are
the commands below the same ones used in the qdec GUI? As far as I
can
tell, they will both give me cortical thickness differences on a
vertex by
vertex basis. There are probably some subtle differences in the
way they
are coded, but any major changes? Thanks.
http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
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Can you update to v4.2.0? I think that TAGskip problem is a bug we fixed, but I can't find when it was fixed in our ReleaseNotes. Also, I thick that version of mri_surf2surf had problems writing .mgh files.
Nick
On Mon, 2009-02-23 at 17:11 -0600, bell0368@umn.edu wrote:
The machine I am running on has 14 GB of memory, is there a limit on the size mri_info will read? Also, from "du" it appears to only take up 1.1M. I am running Freesurfer 4.0 on Centos4.
mri_info 1633_20170_1271/surf/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh TAGskip: failed to calloc 3623878656 bytes!
Cannot allocate memory //////
du -sch 1633_20170_1271/surf/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh
1.1M 1633_20170_1271/sur/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh
1.1M total
On Feb 23 2009, Nick Schmansky wrote:
what version of freesurfer is being used?
type 'freesurfer --version' and its the last line.
On Mon, 2009-02-23 at 14:08 -0600, bell0368@umn.edu wrote:
Thanks for the info. I am getting an error on the mri_surf2surf step of the thickdiffmap.sh script. It occurs whether I use subj1, subj2, fsaverage, or a different person (subj3) in the command below. There was one comment from Bruce in the archives that says this error will occur if the registration is poor. The inter-subject, i.e. subj1_to_subj2, registration is fine, as shown with tkregister2. I am not sure how to quality/error check the registration to the sphere. On a more general note, this step is supposed to resample the cortical difference map to the template subject (--trgsubject), I guess I am a bit unclear as to why sphere.reg is needed, considering that my --trgsubject could be anything, not necessary the standard sphere. Does mri_surf2surf first align the subj1 standard sphere vertices to the --trgsubject and then align the difference map using the same transform? Thanks for any help.
thickdiffmap.sh 1633_20170_1271 1633_20240_1280 fsaverage lh 1 2 3 | tee > output5.log
mri_surf2surf --srcsubject 1633_20170_1271 --sval /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271 /surf/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh --trgsubject fsaverage --tval /home/bfs-raid3/chris/18
2_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20170_1271_to_1633_20240_1280_resampled _to_fsaverage.mgh --hemi lh --surfreg sphere.reg Registration surface changed to sphere.reg srcsubject = 1633_20170_1271 srcval = /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.thickness_diff_1633_20170_12 71_to_1633_20240_1280.mgh srctype = trgsubject = fsaverage trgval = /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20 170_1271_to_1633_20240_1280_resampled_to_fsaverage.mgh trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.sphere.reg Loading source data Segmentation fault (above is in my log file) (below is error printed to the screen) INFO:try to get src info from transform. MRIalloc(1879048192, -1125858646, 317): bad parm Cannot allocate memory
On Feb 23 2009, Douglas N Greve wrote:
Info on doing the paired t is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
Don Hagler wrote:
You could extend the analysis described on that wiki page by calculating tstats and pvalues (in addition to mean and stdev). Then you have a paired t-test, whereas mri_glmfit with qdec would be doing an unpaired t-test. I think preproc has an option to calculate within subject differences for a paired t-test with mri_glmfit as well. As you may know, paired t-tests are more sensitive than unpaired t-tests, and are generally more appropriate when you make within subject comparisons. On the other hand, if you intend your exercise to be a test for the likelihood of false positive differences between groups, the unpaired t-test may be more appropriate.
Subject: Re: [Freesurfer] qdec thickness and repeatability From: nicks@nmr.mgh.harvard.edu To: bell0368@umn.edu Date: Fri, 20 Feb 2009 15:15:10 -0500 CC: freesurfer@nmr.mgh.harvard.edu
The two methods are very different. In the method described on the thickness repeatability page, its computing a mean and stddev of the thickness for your group. This a direct and easily interpretable measure, but doesn't give you a statistical measure (but you could do that on your own with some external package).
In qdec (mri_glmfit), it would be conducting a GLM-based analysis looking for statistical significance, expressed as a p-value at each vertex, in thickness between groups. Here, raw thickness differences are hidden in the analysis.
However, you can of course do both analysis, and compare them, which I would suggest you do. You would hope the areas of change are the same. Note that you can load external surface maps, such as a thickness- diff.mgh map, onto the fsaverage surface in qdec, so that you can view both analysis (or just load the thickness-diff.mgh map in tksurfer).
Its on the list of things to add to qdec to create two-group thickness difference maps, as well as just viewing the mean group thickness, to save some work for this sort of thing.
Nick
On Fri, 2009-02-20 at 12:53 -0600, bell0368@umn.edu wrote: > All, > > I am going to run an analysis of cortical thickness
reproducibility; there
> are at least two methods that seem obvious. I could run qdec
analysis with
> time1 and time2 as different groups or I could run the methods
below. Are
> the commands below the same ones used in the qdec GUI? As far as > I
can
> tell, they will both give me cortical thickness differences on a
vertex by
> vertex basis. There are probably some subtle differences in the
way they
> are coded, but any major changes? Thanks. > > http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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