Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Error with aparcstats2table
by Douglas N Greve 04 Aug '11

04 Aug '11

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(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)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(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>> > > *Cc:* Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>; "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer(a)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(a)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(a)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(a)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(a)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(a)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(a)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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person > to whom it is > > > > addressed. If you believe this e-mail was sent to you in error > and the e-mail > > > > contains patient information, please contact the Partners > Compliance HelpLine at > > > > http://www.partners.org/complianceline . If the e-mail was sent > to you in error > > > > but does not contain patient information, please contact the > sender and properly > > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)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(a)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 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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 > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

1 0

RE;Corrections with the oPTIC NERVE
by Antonella Kis 04 Aug '11

04 Aug '11

Hi Bruce, Many thanks for your answer and for your valuable help. I was just following the the examples from the Free Surfer manual on the page 57 (please see the attachment). I believe my image (the slice I sent you on yesterday) is similar or closed looking with the one on the page 57. Since I am a beginner and you are an expert I will be very grateful if you can let me know your opinion (I am not sure what I should do about correcting this slice). Many thanks, Antonella

2 1

Re: [Freesurfer] Error with aparcstats2table
by Douglas N Greve 04 Aug '11

04 Aug '11

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(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>; > "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)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(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)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(a)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(a)yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>> > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>" > <freesurfer(a)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 > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to > whom it is > > > addressed. If you believe this e-mail was sent to you in error and > the e-mail > > > contains patient information, please contact the Partners > Compliance HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > > > but does not contain patient information, please contact the > sender and properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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(a)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 > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

1 0

Re: [Freesurfer] Correction for the Optic Nerve
by Bruce Fischl 03 Aug '11

03 Aug '11

Hi Antonella, it's hard to say just looking at a single slice. Why do you think you need to correct it? Bruce On Wed, 3 Aug 2011, Antonella Kis wrote: > Hi Bruce, > > I will be very grateful if you or someone else can give me an advise if I should do some corrections for the optic nerve in the following > slice. > > Many thanks, > Antonella > >

1 0

Hippocampus Data
by Sunil Patel 03 Aug '11

03 Aug '11

Hello, I'm looking for a way to extract data from hippocampus labels. I was wondering if there is a simple command that I can use to get the data from the labels between certain slices. If there's not, then I was wondering what the best course of action would be to do so. I need to be able to separate the hippocampus into anterior and posterior sections. Best, Sunil

2 1

Hippocampus Data
by Sunil Patel 03 Aug '11

03 Aug '11

1 0

Hippocampus Data
by Sunil Patel 03 Aug '11

03 Aug '11

1 0

Hippocampus Data
by Sunil Patel 03 Aug '11

03 Aug '11

1 0

How to mesure the medulla, midbrain and pons volume?
by Lucas Lessa 03 Aug '11

03 Aug '11

Dear friends, I'd like to mesure the midbrain volume from some patients using Freesurfer. Is it possible or I can only mesure the brain stain volume? Thnak you. Lucas Lessa.

2 1

"Holes" in the mri_label2vol results
by Shanqing Cai 03 Aug '11

03 Aug '11

Hi, I am using mri_label2vol to generate some volume ROIs from surface labels. I noticed that the results contain "holes", by which I mean voxels that aren't label and are surrounded by labeled voxels. This seems to happen regardless of the step size I specify after the "--proj" option of mri_label2vol and this happens in both the gray- and white-matter projections. I am using FS 5.1.0. I wonder whether other people have experienced similar problems and how these holes can be gotten rid of. Thanks! Best regards, Shanqing Cai

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer