try this mri_segstats --annot bert lh aparc --i lh.thickness --sum lh.aparc.thickness.stats
Antonella Kis wrote:
Dear Doug,
I was running the mri_segstats as you suggested but I got an error:
Constructing seg from annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading lh.aparc.stats mri_read(): couldn't determine type of file /usr/local/freesurfer/subjects/bert/stats/lh.aparc.stats ERROR: loading lh.aparc.stats
This is what I did:
setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/bert/stats mri_segstats --annot bert lh aparc --i lh.aparc.stats --sum lh.aparc.stats
Please help! Thanks Antonella
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Antonella Kis atorok9@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, August 4, 2011 10:39 AM *Subject:* Re: [Freesurfer] Error with aparcstats2table
You can use mri_segstats with the --annot option. The output summary table will have a column with the number of "voxels". In this case, it will actually be number of vertices.
doug
Antonella Kis wrote:
Hi Doug,
Thank you for your help. Based on your answer my questions is: Do I
have to install the MATLAB software on my computer an load the read_annotation.m file from FS? I know MATLAB is not a free software so I wonder if there is another way.
Thanks, Antonella
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*To:* Antonella Kis <atorok9@yahoo.com mailto:atorok9@yahoo.com>;
freesurfer <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent:* Thursday, August 4, 2011 9:58 AM *Subject:* Re: [Freesurfer] Error with aparcstats2table
you can load the annotation into matlab with read_annotation.m doug
Antonella Kis wrote:
Hi Doug,
Thank you very much for your answer. I need to prepare a table
here to include the number of vertex and the cortical thickness, for some further studies. Is there a way to do it in MATLAB? How can I run MATLAB using FS under Linux? I have the startup.m file and a MATLAB directory installed in the freesurfer folder but I don't know how I can run MATLAB using FS.
Thank you very much for your help. Antonella
*From:* 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>>
*To:* Antonella Kis <atorok9@yahoo.com mailto:atorok9@yahoo.com
<mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com>>
*Cc:* Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>; "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>>
*Sent:* Wednesday, August 3, 2011 10:55 AM *Subject:* Re: [Freesurfer] Error with aparcstats2table
Hi Antonella, there is not an option for getting the number of
vertices because that is not a meaningful quantity. Why do you want it?
doug
Antonella Kis wrote:
Hi Bruce,
Sorry to bother you again with the same question. Unfortunately
I did not get any reply from the freesurfer list (from Doug and/or Nick as you mentioned) so I will really appreciate if you can help me with the same question:
in the aparc stats I have for each segmentation the Number of
Vertices, Surface Area, etc.
I want this data to be exported in a table where in the first ro
I will have the thickness of each segmentation(bankssts , etc) and the second row I want the Number of Vertices, for each subject.
Many thanks, Antonella *From:* Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>>
*To:* Antonella Kis <atorok9@yahoo.com
mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com>>>
*Sent:* Friday, July 29, 2011 5:24 PM *Subject:* Re: [Freesurfer] Error with aparcstats2table
doug and nick can help with that On Fri, 29 Jul 2011, Antonella Kis wrote:
Hi Bruce,
Thanks again for helping. I mean in the aparc stats I have for
each segmentation the Number of Vertices, Surface Area, etc. I want this data
to be exported in a table where in the first ro I will have
the thickness of each segmentation(bankssts , etc) and the second row I want the
Number of Vertices, for each subject.
Thanks. Antonella
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>>>
To: Antonella Kis <atorok9@yahoo.com
mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com>> <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com>>>>
Cc: "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>> <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 mailto:freesurfer@nmr.mgh.harvard.edu>>>" <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>> <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 mailto:freesurfer@nmr.mgh.harvard.edu>>>>
Sent: Friday, July 29, 2011 3:18 PM Subject: Re: [Freesurfer] Error with aparcstats2table
Hi Antonella,
what do you mean by no. of vertices? The total # in the
surface? You can get that with mri_info. It's loosely related to surface area, but not
that interested a quantity.
Bruce
On Fri, 29 Jul 2011, Antonella Kis wrote:
Hello everyone,
I was trying to create a table with my statistical results
(the cortical thickness and the number of vertices) and I was running:
aparcstats2table --hemi lh --subjects bert NPI001 --meas
thickness -t lh.aparcstas.THICKNESS.txt
When I tried to also get the number of vertices a table by
running: aparcstats2table --hemi lh --subjects bert NPI001 --meas vertices -t
lh.aparcstas.VERTICES.txt I got the following error:
aparcstats2table: error: option --measure: invalid choice:
'Voxels' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv')
I Why I don't have an option for the no. of vertices?
Can I get a table with both data: cortical thickness and no.
of vertices?
Many thanks, Antonella
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html