Freesurfer October 2011

freesurfer@nmr.mgh.harvard.edu

95 participants
160 discussions

Re: [Freesurfer] roi analysis from label or annotation
by Douglas N Greve 25 Oct '11

25 Oct '11

Did you try passing --olab a full path? Knut J Bjuland wrote: > Hi > > I use mri_surfcluster -olab --subject fsaverage --in sig.mgh --hemi ?h > to produce label for the areas indicated by mri_glmfit. Then I use > label and mean follow by the python script. > > > cheers > Knut J > > I use > > > Date: Mon, 24 Oct 2011 10:43:02 -0400 > > From: greve(a)nmr.mgh.harvard.edu > > To: knutjbj(a)hotmail.com > > CC: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] roi analysis from label or annotation > > > > It's very hard to tell what you are doing without a command-line. > > Generally, you can pass the full path of a label to surfcluster to make > > it save it in a particular location. > > doug > > > > Knut J Bjuland wrote: > > > I am working on roi analysis. I have made a label using > mri_surdcluster and used mri_label2label to > > > copy the label from fsaverage to each individual subject. The next > step would be to use > > > mris_anatomical_stats to calculate stats for each subject. I used > a Python to merge the txt file from > > > mris_anatomical_stats. > > > > > > Is it possible to force mri_surfcluster to save the label another > dir than fsaverage? > > > Can I use convert roi label to annotation and then use aparc2stats > > > or similar command to get group statics? > > > > > > > > > Cheers > > > Knut J > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > 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 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > 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. > > -- 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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Question on mris_pmake
by Jungwon Ryu 25 Oct '11

25 Oct '11

Hi, I'm trying to get distances on a cortical surface between sets of voxels in visual areas and I have two questions; 1) I have the following error message so often; === System error: Address already in use Fatal error encountered. SSocket `Unnamed SSocket_UDP_receive' (id: 0) Current function: c_SSocket_UDP_receive::c_SSocket_UDP_receive Problem binding to socket 1701 Error returned from system: Address already in use Throwing exception to (this) with code 1 terminate called after throwing an instance of 'c_SSocket*' runSh_Ori_1_02_01.sh: line 5789: 93334 Abort trap mris_pmake --subject JR20110819 --hemi rh --surface0 white --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:907,endVertex:731 >> result_Ori_1_02_01.txt === I have around 10,000 voxel pairs to run mris_pmake( ) command. Since I have to call mris_pmake( ) so many times (one pair by one pair), I splitted the whole list of voxel pairs into four script files, containing many mris_pmake commands with 2,500 voxel pairs as arguments, then I ran scripts with four terminal windows saparately to parallelize the processing. All script files are located in the same diretory. Then I had the message as above. What might be the problem? (It seems as if multiple terminal instances share the socket port number) 2) How can I get interhemispheric distances between visual areas across hemispheres? Ryu PhD student Department of Brain and Cognitive Sciences, Seoul National University, Korea

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Re: [Freesurfer] mris_anatomical stats different thickness files
by Douglas N Greve 24 Oct '11

24 Oct '11

no, that would be 15 "smooth steps". If you want to smooth by 15mm, then use mris_fwhm. doug krista kelly wrote: > Would the following code give me data smoothed with 15 fwhm kernel? > > mris_anatomical_stats -l lh.v1.label -t lh.thickness -nsmooth 15 -b -f > BV01/stats/lh.v1_pial.stats BV01 lh pial > > > Thanks! > > > On Mon, Oct 24, 2011 at 10:40 AM, krista kelly > <krista.kelly16(a)gmail.com <mailto:krista.kelly16@gmail.com>> wrote: > > Thanks for clearing this up! It makes a lot more sense now. > > > On Mon, Oct 24, 2011 at 10:35 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > > krista kelly wrote: > > I'm looking at both cortical thickness and surface area > differences between two groups. I've been using > mris_anatomical_stats to retrieve values but had a few > questions: > > 1) Do I need to do separate mris_anatomical_stats using > different thickness files (bolded below) to get cortical > thickness and surface area measures. For example: > > cortical thickness - mris_anatomical_stats -l lh.v1.label > -t *lh.thickness* -b -f BV01/stats/lh.v1.stats BV01 lh > surface area - mris_anatomical_stats -l lh.v1.label -t > *lh.area *-b -f BV01/stats/lh.v1.stats BV01 lh > > > Or, since the output files include all of these measures, > is it fine to just run one of the two? > > Just run the first one. > > > 2) The output files for both analyses run above (with > different thickness files) have identical values for > everything except for tray matter volume. Using > lh.thickness file - grayvol = 8082; using lh.area file - > grayvol = 4029. Can anyone clarify why this happens? > > It computes the gray matter volume by thickness*area. If you > pass it "area" as the "thickness", then you are probably > getting area*area. Though I'm surprised that the "thickness" > values are correct. > > > 3) The default surface area values are for the white > matter surface. How do I run mri_anatomical_stats to get > the pial surface? I've tried mris_anatomical_stats -l > lh.v1.label -t *lh.area.pial *-b -f BV01/stats/lh.v1.stats > BV01 lh but I get identical values for everything (except > grayvol). > > Try adding "pial" to the end of the command line (and use > lh.thickness) > doug > > > Thanks! > Krista > ------------------------------------------------------------------------ > > _______________________________________________ > 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 <tel:617-724-2358> Fax: > 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > > -- 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] white matter volume in a ROI
by Douglas N Greve 24 Oct '11

24 Oct '11

It will be more involved than that. You will need to create an annotation that contains your label (maybe in addition to other labels), then uses mri_aparc2aseg with the --labelwm option, something like mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot doug dolphinede(a)aol.com wrote: > Hi Doug, > > thanks a lot for your answer. > > So i understand you right that i can get "exact" knowledge about the > thickness, grey matter volume and pial surface area in my ROI, but in > case of "the" ROI white matter volume, i have to look to which > cortical label my ROI counts and then I use the wmparc.files for this > label? > > Best regards > > Daniel Klein > > > > > > > > > > -----Ursprüngliche Mitteilung----- > Von: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > An: dolphinede <dolphinede(a)aol.com> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Verschickt: Mo, 24 Okt 2011 4:48 pm > Betreff: Re: [Freesurfer] white matter volume in a ROI > > For GM area and volume, you can use mris_anatomical_stats. See the > recent thread on how. For the WM volume, how would you define the WM > volume that corresponds to you label? We have a routine that parcellates > WM based on closest proximity to a cortical label. > doug > > dolphinede(a)aol.com wrote: > > Dear FreeSurfer experts, > > > > i have created a ROI in qdec , where i have found a significant > > correlation between lgi and age. > > > > I mapped this ROI to all subjects. > > > > I am interested to compare in this ROI the pial-surface area, the grey > > matter volume and if possible the white matter volume for this > > specific region and i am not sure how to do this? > > > > Best regards > > > > Daniel Klein > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > -- 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] implementation on Neurodebian
by Cartik Sharma 24 Oct '11

24 Oct '11

Hi Knut, Good to know we can speed things up with CUDA. I have a multicore CPU and was wondering if there is a parallelized version of Freesurfer on the CPU. Thanks for the speedup! Best regards, Cartik On Oct 24, 2011, at 4:41 AM, Knut J Bjuland wrote: Hi Cartik You use -use-gpu to offload rendering to the GPU using cuda. Knut J > From: Cartik.Sharma(a)childmind.org<mailto:Cartik.Sharma@childmind.org> > To: knutjbj(a)hotmail.com<mailto:knutjbj@hotmail.com> > Subject: Re: [Freesurfer] implementation on Neurodebian > Date: Thu, 20 Oct 2011 15:48:10 +0000 > > Hi Knut: > > Cool..is this speeding up things by rendering on the GPU. > Is there a way to offload computation to the GPU. > > Best regards, > Cartik > > On Oct 20, 2011, at 10:57 AM, Knut J Bjuland wrote: > > > Hi Cartik > > > > If you enable cuda with -use-gpu the recon-all will run faster. > > > > Knut J > > > > Den 17.10.2011 16:41, skrev Cartik Sharma: > >> Dear Freesurfer developer(s), > >> > >> Is there a way to get Freesurfer run faster on Neurodebian. While the package produces > >> some truly out of the world segmentations and labels for the cortical surface, it seems > >> to take time. > >> > >> For eg: > >> Defect correction and retesellation takes an hour, other steps take longer..I'm not sure if > >> it's the original dataset, the OS platform (i.e Virtual Machine, Neurodebian) or original > >> computational engine itself. > >> > >> Would be happy in efforts and hints to make this run faster. > >> > >> Best regards, > >> Cartik Sharma > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> 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. > >> > >> > >> > > >

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aparc2feat with custom annotation file
by Michelle Umali 24 Oct '11

24 Oct '11

Hi Freesurfers, I am trying to generate binary V1 and V2 masks based on my fieldsign results. We created a custom annotation file by adding the two new areas (muuV1 and muuV2, entries 36 and 37, resp., i.e., in Matlab in rows 37 and 38) to the aparc color table using Matlab and setting all labels to zero. Then we marked the areas in tksurfer (imported the annotation file, made closed paths around the vertices, and added it to the muuV1 or muuV2 label) and exported the annotation file. This worked fine, but when we used aparc2feat (on feat data previously registered with regfeat2anat) using the --annot <our_annot> option, only muuV1 (entry 36) was correctly extracted, and there were no entries for label 37 in the resulting volume. Do you have any idea what could have gone wrong? I attached our annotation file (gzipped) containing the marked areas muuV1 and muuV2. Thank you very much, Michelle

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roi analysis from label or annotation
by Knut J Bjuland 24 Oct '11

24 Oct '11

I am working on roi analysis. I have made a label using mri_surdcluster and used mri_label2label to copy the label from fsaverage to each individual subject. The next step would be to use mris_anatomical_stats to calculate stats for each subject. I used a Python to merge the txt file from mris_anatomical_stats. Is it possible to force mri_surfcluster to save the label another dir than fsaverage? Can I use convert roi label to annotation and then use aparc2stats or similar command to get group statics? Cheers Knut J

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mris_anatomical stats different thickness files
by krista kelly 24 Oct '11

24 Oct '11

I'm looking at both cortical thickness and surface area differences between two groups. I've been using mris_anatomical_stats to retrieve values but had a few questions: 1) Do I need to do separate mris_anatomical_stats using different thickness files (bolded below) to get cortical thickness and surface area measures. For example: cortical thickness - mris_anatomical_stats -l lh.v1.label -t *lh.thickness*-b -f BV01/stats/lh.v1.stats BV01 lh surface area - mris_anatomical_stats -l lh.v1.label -t *lh.area *-b -f BV01/stats/lh.v1.stats BV01 lh Or, since the output files include all of these measures, is it fine to just run one of the two? 2) The output files for both analyses run above (with different thickness files) have identical values for everything except for tray matter volume. Using lh.thickness file - grayvol = 8082; using lh.area file - grayvol = 4029. Can anyone clarify why this happens? 3) The default surface area values are for the white matter surface. How do I run mri_anatomical_stats to get the pial surface? I've tried mris_anatomical_stats -l lh.v1.label -t *lh.area.pial *-b -f BV01/stats/lh.v1.stats BV01 lh but I get identical values for everything (except grayvol). Thanks! Krista

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matlab script to convert array back to thickness file format?
by Lara Foland-Ross 24 Oct '11

24 Oct '11

Hi there, We're using load_mgh.m to load several individual (single subject) cortical thickness maps (each 1X163842) that we'll use to compute a group-level statistic in matlab. We're not changing the dimensionality or order of the information loaded and we would like to know if there is a matlab script we might use to convert our resulting (1X163842) array of statistical values back into a .mgh file that can be read on FreeSurfer. Thanks! Lara -- Lara Foland-Ross Postdoctoral Fellow Stanford Mood and Anxiety Disorders Laboratory Department of Psychology Stanford University 450 Serra Mall, Stanford, CA 94305 Jordan Hall, Building 420, Room 142

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cortical surface of individual subject: coordinates in individual's MNI space
by Nela Cicmil 24 Oct '11

24 Oct '11

Dear Freesurfer Developers and Users, I have two question(s) about Freesurfer and individual subject's MNI coordinates: (1) Having run recon-all to reconstruct the cortical surface for an individual subject in my study, is it possible to obtain the list of coordinates that describe the points in the individual subject's MNI space that comprise the cortical surface of that subject's brain? This is in order to run an MEG beamformer analysis (in matlab) in the subject's own MNI space, but restricted to those voxels that comprise the cortical surface for that subject, as calculated by Freesurfer. (2) Once I have obtained (in matlab), for a list of voxels that comprise the cortical surface, each of the their MNI coordinates and their associated activation value (e.g. tstat), is there a straightforward way to display this on the cortical surface of that subject in tksurfer, for example by converting to a simple wfile? I searched the archives but could not find information that explained this directly; apologies if this does already exist: if so, could you please point me towards it? Thank you so much for your help, Best wishes, Nela ---- Nela Cicmil D.Phil Candidate, Neurophysiology Dept. Physiology, Anatomy & Genetics University of Oxford Tel: 01865 282274 Internal: 82274

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Freesurfer October 2011