Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Can I use freesurfer to segment a phantom
by John Jan Drozd 04 Aug '11

04 Aug '11

Hi, I have MRI scans of a plastic polycarbonate ventricle that is an actual shape of a ventricle. It is in a brain mold of agar gel solution. I segmented the ventricle successfully using multiple seeds fuzzy connectedness in ITK. My segmentation was 97.2 % accurate. In ITK it had only single seed fuzzy connectedness but I adapted the code to work with multiple seeds. The reviewers of our paper want us to use FreeSurfer to segment the ventricles. Can I use freesurfer when the brain mold only has ventricles and grey matter (agar gel)? Or does Freesurfer require the brain to have the same number of brain parts as the Talairach atlas that it uses? My hunch us that it is the latter case. Thank you for your time. John John Drozd Post-Doctoral Fellow Robarts Research Institute University of Western Ontario London, Ontario, Canada http://publish.uwo.ca/~jdrozd2

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

04 Aug '11

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(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)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(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>>; > freesurfer <freesurfer(a)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(a)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(a)yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>> > > > *Cc:* 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>>>; "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:* 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>> > <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>>>> > > > > *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>>> > <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(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>>> <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(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>>> > <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(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>>> > <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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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>> > <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(a)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 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> > <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

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Which hemisphere is in the sagital view of the wm
by Antonella Kis 04 Aug '11

04 Aug '11

Hi, When visualizing the wm.mgz in the coronal view we can see both hemispheres: lh and rh. How do I know which hemisphere I am visualising in a sagittal view? Do I have a transition from lh to the rh while passing through the slices? Thank you, Antonella

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Re: [Freesurfer] trac-all -path errors
by Moiyadi, Ammar 04 Aug '11

04 Aug '11

Hi - The txt files are missing for all the tracts as it turns out trac-all -prep exited with errors before getting to -prior. It appears there is a problem with my bvec file since the dmri/bvec is reading all 0's. As a result, i get this error "Error: bvecs and bvals don't have the same number of entries". I have attached my bvec.txt file and trac-all log - any ideas to where the problem may lie? Thank You, Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] Sent: Monday, August 01, 2011 12:32 PM To: Moiyadi, Ammar Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -path errors Hi Ammar - Yes, -prior is the last step included in -prep. Are the text files missing for all tracts, or specifically for lh.cst? Thanks, a.y On Mon, 1 Aug 2011, Moiyadi, Ammar wrote: > Hi, > I am also getting the error where the txt files cannot be opened because they were not created beforehand. Where does the trac-all -prior step take place? Does it appear within the trac-all -prep script? > > Thank you, > > Ammar Moiyadi, BS > Professional Research Assistant > Department of Psychiatry > University of Colorado Anschutz Medical Campus > 303-724-5490 > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] > Sent: Friday, July 29, 2011 10:00 AM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 89, Issue 99 > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. trac-all -path errors (Ping-Hong Yeh) > 2. Re: trac-all -path errors (Priti Srinivasan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 29 Jul 2011 11:09:28 -0400 > From: Ping-Hong Yeh <pinghongyeh(a)gmail.com> > Subject: [Freesurfer] trac-all -path errors > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAL1NnmP2+KdE5cNMVH4-qhnvSeMeQA7AjQ+cp-qPFtmGv3A+0Q(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > I got the error running "trac-all -path -c configure.txt" > > ERROR: Could not open > ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt > > > I can only find only image files in the "dlabel/diff" directory, but > not text files. > > Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? > > Thanks, > > Ping > > > ------------------------------ > > Message: 2 > Date: Fri, 29 Jul 2011 11:26:13 -0400 (EDT) > From: "Priti Srinivasan" <rspriti(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] trac-all -path errors > To: "Ping-Hong Yeh" <pinghongyeh(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <42727.132.183.139.239.1311953173.squirrel(a)mail.nmr.mgh.harvard.edu> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Ping, > > The text files get created in the trac-all -prior stage. Maybe something > went wrong in that step. Is this the case for all the tracts or just for > this tract? If you can send us the trac-all.log file under the scripts > directory it'll be easier to troubleshoot as to what went wrong. > > -Priti > > >> Hi, >> >> I got the error running "trac-all -path -c configure.txt" >> >> ERROR: Could not open >> ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt >> >> >> I can only find only image files in the "dlabel/diff" directory, but >> not text files. >> >> Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? >> >> Thanks, >> >> Ping >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 89, Issue 99 > ****************************************** > > > 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Bbregister & retinotopy
by Michelle Umali 04 Aug '11

04 Aug '11

Dear Freesurfers, I've been troubleshooting my bizarre looking fieldsign data. I ran bbregister for my polar and eccentricity images, then re-ran the retinotopy analysis. The data still look the same. The fieldsign image is still a mass of blue and red speckles. Any tips on how I should proceed? Thanks. Michelle

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Re: [Freesurfer] RE; Attachment for the OPTIC NERVE corrections
by Bruce Fischl 04 Aug '11

04 Aug '11

Hi Antonella, try running things all the way through, then the only stuff you need to fix is if the surfaces are not visually in the right place. cheers Bruce On Thu, 4 Aug 2011, Antonella Kis wrote: > Sorry I forgot to attach the manual so you can compare the image on the page > 57 with my slice. > > Thanks. > > > 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 > > > > >

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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

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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

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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

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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 > >

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