Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Re: [Freesurfer] mri_surf2surf error
by mdkruepke＠uwalumni.com 01 Jun '12

01 Jun '12

Bruce- Here you go. Subjects recoded. Graph: name Data: path Variable: Subject Measurement: external subject id, class id, variable value, measurement value, standard deviation ------------ S1 Cl1 0.0 3.10522500831 0.268702566292 S2 Cl1 1.0 2.67585065105 0.396833961125 S3 Cl1 2.0 3.07631433273 0.173949345568 S4 Cl1 3.0 2.85668014067 0.0907729539181 S5 Cl1 4.0 3.24184323479 0.212597547853 S6 Cl1 5.0 2.54176559894 0.111183384791 S7 Cl1 6.0 2.87165045086 0.137271513295 S8 Cl1 7.0 2.72165358457 0.128648203321 On 6/1/12, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > something like this: > > head ~/local_subjects/bruce/label/rh.cortex.label > #!ascii label , from subject vox2ras=TkReg > 141813 > 0 11.129 -93.761 -16.820 0.0000000000 > 1 11.136 -93.912 -16.623 0.0000000000 > 2 10.755 -93.913 -16.573 0.0000000000 > 3 11.696 -93.374 -17.237 0.0000000000 > 4 11.022 -93.203 -16.969 0.0000000000 > 5 11.020 -93.855 -17.042 0.0000000000 > 6 10.248 -93.745 -16.712 0.0000000000 > 7 11.591 -93.603 -17.551 0.0000000000 > > > > and please cc the list so others can answer! > On Fri, 1 Jun 2012, > mdkruepke(a)uwalumni.com wrote: > >> Bruce- >> The partition does not appear to be full, although we have been having >> issues with migrating data so >> that could be a source of the issue. The rh.cortex.label does exist and is >> located within the subject's >> label dir. As for the first couple of lines, I am unsure what you are >> asking for. >> >> Thanks for the quick response! >> >> Best- >> Michael >> >> On Fri, Jun 1, 2012 at 10:26 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Michael >> >> can you check to see that your partition is not full? Does the >> rh.cortex.label file exist >> in that subject's label dir? If so, what are the first couple of >> lines? >> >> cheers >> Bruce >> >> On Fri, 1 Jun 2012, mdkruepke(a)uwalumni.com wrote: >> >> To anyone who can help - >> I am trying to tun a GLM on a set of data and am currently >> receiving an error >> during the mri_surf2surf >> portion. When running this portion i receive an error ( could >> not scan # of >> lines from (path to >> rh.cortex.label)). This does not happen when running this >> portion for the lh, >> only the right. I am >> unable to find any information on this error on the mailing >> list so im hoping >> someone can help! >> >> Best- >> Michael Kruepke >> >> -- >> Michael D. Kruepke >> PhD - University of Illinois at Urbana-Champaign >> BA - Psych - University of Wisconsin-Madison >> mdkruepke(a)gmail.com >> (262)-483-7449 >> >> >> >> >> >> 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. >> >> >> >> >> -- >> Michael D. Kruepke >> PhD - University of Illinois at Urbana-Champaign >> BA - Psych - University of Wisconsin-Madison >> mdkruepke(a)gmail.com >> (262)-483-7449 >> >> >> -- Michael D. Kruepke BA-Psychology University of Wisconsin-Madison mdkruepke(a)uwalumni.com (262)-483-7449

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Re: [Freesurfer] mri_vol2surf masking
by Kathryn I. Alpert 01 Jun '12

01 Jun '12

Hi Doug, I was wondering if it was possible to have the intensity at the nearest non-zero voxel projected onto the vertex. Perhaps if we use --projfrac 0.5, mri_vol2surf will select mostly GM voxels, which is our goal. Thanks, Kate On 06/01/2012 12:47 PM, Douglas N Greve wrote: >What do you mean ignore? If you mask them out of the volume so that they >are 0 (or -999), then they will be 0 or -999 in the output. >doug > >On 06/01/2012 12:25 PM, Derin J Cobia wrote: >> Bump. >> >> I'm interested in the answer to this question as well. Doug/Bruce, do >> you know? >> >> -Derin >> >> >> On May 29, 2012, at 8:43 PM, Kathryn I. Alpert wrote: >> >>> Dear Freesufer experts, >>> >>> I am wondering if it is possible to tell mri_vol2surf to ignore >>> certain voxels in the src volume, for instance, by setting their >>> intensity to -999. >>> I'm trying to project only gray matter voxels from a PET scan onto >>> the fsaverage surface, but when I use an only-GM PET image as the >>> src, the zeroed-out WM/CSF voxels are occasionally projected onto the >>> surface (with --interp nearest). >>> Any suggestions? >>> >>> Thanks! >>> Kate >>> _______________________________________________ >>> 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. >> >> >> >> _______________________________________________ >> 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 >gr...(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 > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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(no subject)
by Kathryn I. Alpert 01 Jun '12

01 Jun '12

Dear Freesufer experts, I am wondering if it is possible to tell mri_vol2surf to ignore certain voxels in the src volume, for instance, by setting their intensity to -999. I'm trying to project only gray matter voxels from a PET scan onto the fsaverage surface, but when I use an only-GM PET image as the src, the zeroed-out WM/CSF voxels are occasionally projected onto the surface (with --interp nearest). Any suggestions? Thanks! Kate

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Re: [Freesurfer] transfer annot files from template to each subject
by Leon 01 Jun '12

01 Jun '12

Hi, Bruce Thank you very much for your information and the codes. Best Leon ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Leon <leonado78(a)yahoo.com> Sent: Friday, June 1, 2012 10:48 AM Subject: Re: [Freesurfer] transfer annot files from template to each subject p.s. here's a gzipped version of mris_make_face_parcellation you can try out On Thu, 31 May 2012, Leon wrote: > Hi, Bruce > > Here is the information of my linux: > > Linux version 2.6.18-308.4.1.el5 (mockbuild(a)hs20-bc2-4.build.redhat.com) (gcc version 4.1.2 20080704 > (Red Hat 4.1.2-52)) #1 SMP Wed Mar 28 01:54:56 EDT 2012 > I think that I have figured out how to realize that by checking the archives. I first used > mri_surf2surf to transfer ROIs from the template surface to subjects' surfaces, and then used > mri_label2vol to transfer the ROIs from each subject's surface to its volume. Correct me if I am not > heading toward the right direction. > > Going back to llc_make_face_parcellation, if it cannot be used to transfer ROIs between subjects, what > is the difference between providing ?h.sphere and ?h.sphere.reg as the input surface? > > Thanks again for your help! > Leon > > _______________________________________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Leon <leonado78(a)yahoo.com> > Cc: FreeSurfer <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Thursday, May 31, 2012 2:37 PM > Subject: Re: [Freesurfer] transfer annot files from template to each subject > > Hi Leon > > we can give you a version of mris_make_face_parcellation if you tell us what hardware/software > environment you are running in, but it doesn not transfer annotations from one subject to another. For > that you should use mri_surf2surf (I thought mri_label2label did this also, but I guess not). > > cheers > Bruce > > > On Wed, 30 May 2012, Leon wrote: > > > Hi, Bruce > > > > Thank you for the information. I went through the archive again and found > > this post (see below). It seems that this is exactly what I want to do. > > However, I tried mris_make_face_parcellation and found that with my 5.1 > > version, no matter what my input is (?h.sphere or ?h.sphere.reg), I always > > get identical results, same as Franz. Do you know how I can get the updated > > version of the function in which the bug has been fixed? > > > > Also, I have the same question as Franz does: (1) which is a better way to > > transfer annotation file (here is ic?.tri), using mri_surf2surf or using > > mris_make_face_parcellation with the input surface of ?h.sphere.reg? > > (2) I tried mri_label2label and it seems it does not read annotation file. > > Could you let me know why I should use mri_label2label instead of > > mri_surf2surf with "-sval-annot" option? > > > > Sorry for so many questions as I am new to FreeSurfer and your help is > > greatly appreciated! > > Leon > > > > > > > > > > > > Re: [Freesurfer] mris_make_face_parcellation > > > > Franz Liem > > Mon, 13 Feb 2012 05:35:10 -0800 > > > > Dear Bruce, > > > > thank you so much for your reply; it seems to work now. > > > > However, a weird thing, I also mentioned in my previous post, still happens: > > when using ic3 there are duplicate labels in the newly created annotations. > > > at least the following labelnames are given to two spatially separated > > > labels. > > > ic3.tri_vertex_25 (in fsaverage lh: cluster 1 around vertex 41132, cluster > > 2 > > > around vertex 157199) > > > ic3.tri_vertex_42 (in fsaverage lh: cluster 1 around vertex 137845, > > cluster 2 > > > around vertex 155417) > > > > Is there a way to avoid this? > > > > Thanks for your help, > > Franz > > > > > > Am 26.01.2012 um 14:47 schrieb Bruce Fischl: > > > > > Hi Franz > > > > > > looks like this was a bug in mris_make_face_parcellation, which I just > > > fixed. It was always using the sphere regardless of what you specified. > > > Krish: can you get Franz a new mac version of it to try out? > > > > > > sorry > > > Bruce > > > > > > > > > On Thu, 26 Jan 2012, Franz Liem wrote: > > > > > >> Dear Freesurfers, > > >> > > >> I have some questions regarding mris_make_face_parcellation (and possibly > > >> found one error in the .tri file). > > >> (I am working with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0). > > >> > > >> I would like to make a high res parcellation of several subjects and used > > >> ic3.tri. Parcels should correspond across subjects. > > >> I computed mris_make_face_parcellation ../surf/lh.sphere > > >> $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot > > >> > > >> 1. It seems not to make a difference whether I choose .sphere or > > >> .sphere.reg as input, the resulting parcellations are identical (i > > checked > > >> by comparing vertex label values in matlab; .inflated deviates a bit, but > > >> not substantially). > > >> According to Bruce > > >>(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18509.html) > > > > >> "You want to use either ?h.sphere if you want it to be uniform in subject > > >> space or ?h.sphere.reg if you want the parcels to correspond across > > subjects" > > >> > > >> Could anybody tell me how the parcellation is performed exactly? I > > thought > > >> it was performed on the input surf (the input surf is parcellated into > > >> (e.g.) 642 equally sized parcels), which should lead to different results > > at > > >> .sphere and .sphere.reg, shouldn't it? > > >> > > >> Alternatively, would it be better to mris_make_face_parcellation the > > >> fsaverage and mri_surf2surf the high res parcellation onto each subject > > to > > >> get cross-subject correspondency (I tried this. It didn't look that great > > >> with this command: mri_surf2surf --srcsubject fsaverage --sval-annot > > >> ic3.annot --trgsubject subject1 --tval ic3s03.annot --hemi lh )? > > >> > > >> To recap, what is the best strategy to arrive with > > >> cross-subject-corresponing parcellations? Performing > > >> mris_make_face_parcellation with ?h.sphere.reg for each subject > > individually? > > >> > > >> 2. There seems to be duplicate structNames/annotationValues when applying > > >> mris_make_face_parcellation with ic3.tri > > >> In fsaverage at least the following labelnames are given to two spatially > > >> separated labels. > > >> ic3.tri_vertex_25 (cluster 1 around vertex 41132, cluster 2 around vertex > > >> 157199) > > >> ic3.tri_vertex_42 (cluster 1 around vertex 137845, cluster 2 around > > vertex > > >> 155417) > > >> How come? > > >> > > >> > > >> Thanks for you help, > > >> Franz > > >> > > >> > > >> _______________________________________________ > > >> 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 > > > > > > > > > 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 > > > > ____________________________________________________________________________ > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > To: Leon <leonado78(a)yahoo.com> > > Cc: FreeSurfer <freesurfer(a)nmr.mgh.harvard.edu> > > Sent: Wednesday, May 30, 2012 3:02 PM > > Subject: Re: [Freesurfer] transfer annot files from template to each subject > > > > Hi Leon > > > > I think mri_label2label should do the trick > > > > cheers > > Bruce > > On Wed, 30 May 2012, Leon wrote: > > > > > Hi, FreeSurfer expert > > > I am having difficulty finding the functions that transfer an annotation > > file I generated on a template to > > > each subject. This template has been registered with several subjects > > using a surface-based registration > > > method. Now what I want is to (1) transfer this annotation file from the > > template to each subject, through > > > surface-based registration. and then (2) transfer the annotation file in > > each subject's surface to their T1 > > > volume space. > > > > > > Could someone show me which functions I need to use? Do I have to convert > > the annotation files first to label > > > files to do that? > > > > > > Many thanks in advance > > > > > > Leon > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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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tkregister question
by Shay Ohayon 01 Jun '12

01 Jun '12

Hi, Here's a question to Doug / anyone else who mastered the intricate way of volume transformations: I'm a bit puzzled. According to Free surfer's documentation (fscoordinates.pdf), the way two volumes are registered to each other using tkregister is always using the fixed transformation (tkvox2ras) (see page 6). However, when I do the following little experiment (using matlab's freesurfer API) A = '001.nii'; B = '002.nii'; X=MRIread(A); X.vox2ras0(1,4) = 40; MRIwrite(X,B); tkregister2 --targ 001.nii --mov 002.nii --regheader -reg R.reg The two volumes are not in alignment when they are loaded into tkregister. Now, what am I missing here? If both were loaded using the fixed transform, they should still be in alignment (i.e., vox2ras should be ignored for registration purposes). Thanks in advance, -- Shay Tsao lab Caltech

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qdec: selecting multiple continuous variables
by Laura M. Tully 01 Jun '12

01 Jun '12

Hi, I am using freesurfer 5.1.0 and qdec 1.4. I'm interested in looking at between group differences in thickness in relation to two other continuous measures whilst controlling for ICV. However, qdec doesn't seem to let me select more that one continuous variable even though I only have group selected (discrete) and ICV (nuisance) as additional variables (i.e. a total of three selected) - it's my understanding that qdec allows up to 4 variables, is there a method to selecting multiple continuous variables that I am missing (e.g. hold down shift and select)? Thanks! Laura. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully(a)fas.harvard.edu -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

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recon all error MRISread: could not open file
by Diana Omigie 01 Jun '12

01 Jun '12

I am getting an error during the recon all step that I cannot figure out. It seems to occur in the stage where labels are being written as two label files are missing in the labels directory ( lh.entorhinal_exvivo.label and lh.entorhinal_exvivo.label ) and an error log message emerges in the labels directory which says: MRISread(/neurospin/meg/meg_ rep/anat/freesurfer_segmentation/lh.EC_average/surf/lh.sphere.reg): could not open file In the main directory,an rh.EC_average and lh.EC_average file appears with broken links... Does anyone know what the problem might be be. Sorry for my ignorance. Many thanks, Diana Omigie

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mri_surf2surf error
by mdkruepke＠uwalumni.com 01 Jun '12

01 Jun '12

To anyone who can help - I am trying to tun a GLM on a set of data and am currently receiving an error during the mri_surf2surf portion. When running this portion i receive an error ( could not scan # of lines from (path to rh.cortex.label)). This does not happen when running this portion for the lh, only the right. I am unable to find any information on this error on the mailing list so im hoping someone can help! Best- Michael Kruepke -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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transfer annot files from template to each subject
by Leon 01 Jun '12

01 Jun '12

Hi, FreeSurfer expert I am having difficulty finding the functions that transfer an annotation file I generated on a template to each subject. This template has been registered with several subjects using a surface-based registration method. Now what I want is to (1) transfer this annotation file from the template to each subject, through surface-based registration. and then (2) transfer the annotation file in each subject's surface to their T1 volume space. Could someone show me which functions I need to use? Do I have to convert the annotation files first to label files to do that? Many thanks in advance Leon

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[Fwd: mri_glmfit error]
by YUMI MAEDA 01 Jun '12

01 Jun '12

HI, I figured out, one of the cope file had problem... YUMI HI, I am trying to see difference in groupmap between 2 time-point within 1 group with glmfit. I followed the instruction"PairedAnalysis". mris_preproc .... --paired-diff mri_glmfit --surf fsaverage "$hemi" --y "$hemi"_cope1_"$grp".sm"$fwhmsrc".mgh --yffxvar "$hemi"_varcope1_"$grp".sm"$fwhmsrc".mgh --glmdir $fsdir/group_surf//"$hemi"_cope"$num"_"$grp".sm"$fwhmsrc"_ffx --ffxdof 1872 --osgm When I checked the output of the mri_glmfit, the mask file does not cover the entire brain as the cope/varcope does. it is much smaller and missing parietal brain. the log file says "Reshaping mriglm->mask..." Is this the issue? YUMI _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer June 2012