Freesurfer

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FW: [Freesurfer] ?h.volume files
by Juergen Haenggi 12 Sep '07

12 Sep '07

Dear Bruce, dear Freesurfer users Thanks a lot for the advice. But when using mri_concate in order to average the volumes, there is the following error: "Error: dimension mismatch" between the lh.volume files of the subjects. We used following syntax: [thickness, f] = read_curv('lh.thickness') ; [area, f] = read_curv('lh.area') ; volume = thickness .* area; write_curv('lh.volume', volume, nfaces); mri_concat --i Subjects_*_Kopie/surf/lh.volume --o average_lh_volume --mean ERROR: dimension mismatch between Subjects_Control01_Kopie/surf/lh.volume and Subjects_Control02_Kopie/surf/lh.volume Thanks in advance Best regards Juergen On 11.9.2007 23:24 Uhr, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > read_curv will return that also: > > [thickness_vector, nfaces] = read_curv('lh.thickness') ; > > I'm a bit worried that you have a dimension mismatch. That shouldn't > happen. > > Bruce > > > On Tue, 11 Sep 2007, Juergen Haenggi, > Psychological Institute wrote: > >> Dear Freesurfer users >> >> I computed ?.volume files by using several commands sent by Bruce. Instead of >> using the save_mgh.m command, which not really worked because there was a >> dimension mismatch later when using mri_concat, we used write_curv.m. I need >> the number of faces in the surface to write ?h.volume files. Where can I get >> these numbers? Is it the file called f created in the Matlab current >> directory after running read_curv multiplying area times thickness, and >> write_curv? >> >> Thanks in advance >> Best regards >> Juergen Haenggi >> >> ------------------------------------------------- >> Juergen Haenggi >> Ph.D. (Dr. des.) >> Division of Neuropsychology >> Institute of Psychology >> University of Zurich >> Binzmuehlestrasse 14, PO Box 25 >> 8050 Zurich, Switzerland >> 0041 44 635 73 97 (phone office) >> 0041 76 445 86 84 (phone mobile) >> 0041 44 635 74 09 (fax office) >> BIN 4.D.04 (office room number) >> j.haenggi(a)psychologie.uzh.ch (email) >> http://www.psychologie.uzh.ch/neuropsy/ (website) >> http://www.juergenhaenggi.ch (private website) >> ------------------------------------------------- >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------- ------ End of Forwarded Message

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Spherical ROIs areas in the fsaverage
by jorge luis 12 Sep '07

12 Sep '07

Hello all I have made changes in the thickness values in some regions of a left hemisfere of a subject surface after mapped it onto the fsaverage sphere. The changes were made to have areas close to these in the left colum of the following table: My area Freesurfer number of vertices 20 mm2 27.88 mm2 (37) 30 mm2 35.09 mm2 (47) 40 mm2 39.17 mm2 (52) 50 mm2 56.89 mm2 (76) 60 mm2 44.05 mm2 (59) I computed the region areas in the fsaverage surface by adding the areas of the triangular faces inside these regions using the spherical coordinates of the vertices and the Heron formula for the triangle area. The freesurfer sphere mapping is based in minimal metric distortion, so, why the freesurfer computed areas for these regions are different(the second column in the table)? In both cases the same surface vertices were found to be inside of the regions (the third column in the table) I would like to have more insight on how freesurfer compute the area of a given ROI in the fsaverage spherical surface. In advance thank you ____________________________________________________________________________________ Sé un Mejor Amante del Cine ¿Quieres saber cómo? ¡Deja que otras personas te ayuden! http://advision.webevents.yahoo.com/reto/entretenimiento.html

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Segmentation Probability Values
by James N. Porter 11 Sep '07

11 Sep '07

Hello FreeSurfers- At any point in the recon-all processing stream does a voxel by voxel map of segmentation probability values get generated? If not, are that at all obtainable through post-processing methods? -- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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?h.volume files
by Juergen Haenggi, Psychological Institute 11 Sep '07

11 Sep '07

Dear Freesurfer users I computed ?.volume files by using several commands sent by Bruce. Instead of using the save_mgh.m command, which not really worked because there was a dimension mismatch later when using mri_concat, we used write_curv.m. I need the number of faces in the surface to write ?h.volume files. Where can I get these numbers? Is it the file called f created in the Matlab current directory after running read_curv multiplying area times thickness, and write_curv? Thanks in advance Best regards Juergen Haenggi ------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -------------------------------------------------

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Fwd: Re: [Freesurfer] Average Volume
by Rafael Huber 11 Sep '07

11 Sep '07

---------- Forwarded message ---------- From: Rafael Huber <rafael(a)huberworld.ch> Date: 11.09.2007 09:19 Subject: Re: Re: [Freesurfer] Average Volume To: Doug Greve <greve(a)nmr.mgh.harvard.edu> Hy Doug, Thank you for your help. I tried to do it with your advice, but when i runned "mri_concat --i SUBJECTS*/surf/lh.volume.mgz --o lh.volume --mean" i always got an error message called "ERROR: dimension mismatch between SUBJECT1/surf/lh.volume.mgz and SUBJECT2/surf/lh.volume.mgz". I created all the volume.mgz files in the same way in matlab. Do you have an idea? Thanks in advance. Best Regards Rafael 2007/9/4, Doug Greve <greve(a)nmr.mgh.harvard.edu>: > > Try following the instructions for doing a thickness study, ie, run > mris_preproc specifying lh.volume.mgz as the measure, then run either > mri_glmfit with --osgm or run mri_concat with --mean. > > doug > > > > > On Mon, 3 Sep 2007, Rafael Huber wrote: > > > Our goal is to get a file of average volume. As i understand the make > > average command it takes the whole information of e.g. ?h.thickness > > out of every /surf folder of every subject and creates an average > > ?h.thickness file and saves it to /average/surf. i try to do the same > > with the ?h.volume.mgz files, which we created with the matlab command > > you proposed us. we made it as far that we have two ?h.volume.mgz > > files in each subjects surf folder and we would like to continue the > > group analyses process. > > > > > > Hi Rafael, > > > > sorry, I don't understand. What do you mean " Problems appeared later > > on, because we didn't find a difference in the average folder compared > > to using the command without lh.volume.mgz files in the surf folder." > > What problems? What kind of differences are you looking for and how? > > > > Bruce > > > > > > On Mon, 3 Sep 2007, Rafael Huber wrote: > > > > Dear freesurfer users > > > > Do you have an idea how to create an average ?h.volume file? > > > > Our goal is to create a file with average volumes for our subjects, to > > follow the group analysis. We know that the idea of using a volume > > measure isn't implemented in the freesurfer software. We runned the > > make_average_subject command in hope to find something like an > > ?h.volume file in the average folder as there are files for the other > > measures like thickness, area, curvature. > > Before we runned the make_average command we followed the advice of > > Bruce Fischl to create .mgh files in matlab with the following > > command: > > > > [thickness, f] = read_curv('lh.thickness') ; > > [area, f] = read_curv('lh.area') ; > > volume = thickness .* area; > > save_mgh(volume, 'lh.volume.mgz', eye(4)); > > > > This functioned very well and we got our lh.volume.mgz files in the > > surf folder. Problems appeared later on, because we didn't find a > > difference in the average folder compared to using the command without > > lh.volume.mgz files in the surf folder. We're now not sure if we > > should continue like normal, or what exactly to do. Has somebody an > > idea. > > > > Best regards > > > > Rafael Huber > > _______________________________________________ > > 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 > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Rafael Huber Student Division of Neuropsychology Institute of Psychology University of Zurich

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running time v4
by ppj＠netfilter.com.br 10 Sep '07

10 Sep '07

Hi, I would like to ask if there's already a benchmark performance of V4 compared to V3. In my environment V3 run a full recon-all in 21 hours full brain. How long I should expect the running time of V4 if I install it? Thanks, Pedro Paulo Oliveira Jr.

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variability
by Leila BH 10 Sep '07

10 Sep '07

Hello, Is there any paper talking about the variability of the used methods (on reconall )? Especially the parcellation? If I reprocess one subject 10 times with the same Freesurfer version, should I expect the same result for parcellation? The freesurfer version that I use is stable3 I tried to see if the parcellation of the new Freesurfer version is similar (visually) to the stable3, and it was very different, is the parcellation method the same in both version? thanks

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Freesurfer and Gaussian Random field theory
by jorge luis 10 Sep '07

10 Sep '07

Hello all I have computed and smoothed some thickness maps using Freesurfer. Next I would like to make inference using Gaussian Random Field theory (GRFT). How can I do it in Freesurfer? If it is not implemented in freesurfer , is there any thing that I have to take into account when applying any GRFT implementation to the statistical parametric thickness maps resulting from Freesurfer analysis? In advance thank you ____________________________________________________________________________________ Sé un Mejor Amante del Cine ¿Quieres saber cómo? ¡Deja que otras personas te ayuden! http://advision.webevents.yahoo.com/reto/entretenimiento.html

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Switch hemispheres
by Inês Souta 09 Sep '07

09 Sep '07

Hi, After processing the hole image I realized that the orientation of the original .mgz file was wrong and I've ended up with switched hemispheres. The right hemisphere is where the left should be, and vice-versa. Otherwise the orientation is right. Since I've already made manual edits, is the anyway of switching hemispheres without having to re-process the hole image again? Thanks, Ines

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RE: [Freesurfer] variability
by rahul＠nmr.mgh.harvard.edu 09 Sep '07

09 Sep '07

Hi Leila, Have you noticed other differences in the same subject using V4 vs V3 (i.e. gray/white bounday differences, thickness thickness difference, etc.) using the same subject? The V4 parcellation should theoretically not be much different from the V3 scheme with the exception of improvement in certain areas such as the anterior cingulate, entorhinal, and the inferior parietal lobule. Where exactly do you find the most amount of difference between the two versions? Best, rahul > Hi Leila, > > do you see this in other subjects? We also have a utility > (mris_divide_parcellation) for automatically dividing each parcellation > unit along it's long axis. > > Bruce > > On Sun, 9 Sep 2007, Leila BH wrote: > >> Hi Bruce, >> Thanks for your answer, >> Actually I reprocessed on subject (I have choose one case who doesn't >> need >> any editing) and the parcellation result is more accurate in midline but >> worst in some other part, is it just by chance? That's why I am asking >> about >> the variability(in version 3 /and between V3 and V4). I attached 2 tif >> files >> for more precision. (one is done with vesion3 and one version4) >> In my work I have to parcellate the cortex on 1000 small ROIs, I use >> freesurfer to do that, based on the 35 parcellation, I subdivide each >> one on >> small rois, so my small ROIs are not really based on gyrus and sulcus, >> and >> to validate my method I want to know the 'error' or variability of the >> original 35-parcellation. Do you suggest me to run one subject N times >> to >> see that? Or do you already know the variability of all the Freesurfer >> pipeline (till the parcellation)? >> thanks >> >> >> -----Original Message----- >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> >> Sent: samedi, 8. septembre 2007 03:24 >> To: Leila BH >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] variability >> >> Hi Leila, >> >> Xiao Han's NeuroImage paper discusses thickness variability, and we've >> looked at parcellation variability in-house, but I don't think we've >> published on it. The V4 parcellation is should be a bit more accurate at >> the midline, but not substantially different. >> >> cheers, >> Bruce >> On Wed, 5 Sep 2007, Leila BH >> wrote: >> >>> Hello, >>> >>> Is there any paper talking about the variability of the used methods >>> (on >>> reconall )? Especially the parcellation? If I reprocess one subject 10 >> times >>> with the same Freesurfer version, should I expect the same result for >>> parcellation? >>> >>> The freesurfer version that I use is stable3 >>> >>> >>> >>> I tried to see if the parcellation of the new Freesurfer version is >> similar >>> (visually) to the stable3, and it was very different, is the >>> parcellation >>> method the same in both version? >>> >>> thanks >>> >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > >

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