Still stuck - I downloaded the bin for mris_left_right_register from https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_left_right_register and ran it from the fsaverage surf directory:
$PROJECTDIR/mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right (Yes, it really should be in $FREESURFER_HOME, but I don't think that's the problem.) it fails with: $Id: mris_left_right_register.c,v 1.2 2011/12/16 20:49:37 greve Exp $ $Id: mrisurf.c,v 1.781 2016/06/13 21:20:50 fischl Exp $ reading lh surface from lh.sphere... reading rh surface from rh.sphere... MRISreadCurvature: could not open ./rh.inflated.H No such file or directory /r2/users/fspace2/abby/AV_6rois/3_experiment/3_analysis/scripts/problabels/mris_left_right_register: could not read curvature file './rh.inflated.H' No such file or directory There is indeed no rh.inflated.H (or lh.inflated.H) in the surf directory. What's my next piece of backtracking? Thanks, Abby > Date: Tue, 3 Apr 2018 15:36:22 -0400 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 170, Issue 1 > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <39459d44-cf44-6a53-1f0f-2eab5c471...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8"; format=flowed > > you can generate them with > > cd $FREESURFER_HOME/subjects/fsaverage/surf > > mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right > rh.sphere.left_right > > should take less than an hour to run > > On 04/03/2018 03:28 PM, Abigail Noyce wrote: > > > > Date: Mon, 2 Apr 2018 14:55:47 -0400 > > From: Douglas Greve <dgr...@mgh.harvard.edu > > <mailto:dgr...@mgh.harvard.edu>> > > Subject: Re: [Freesurfer] mirroring fsaverage labels between > > ? ? ? ? hemispheres > > > > If you have a label defined on the lh or rh of fsaverage, you can > > map it > > to the contralateral hemi with something like > > > > mris_apply_reg --src-label lh.your.label --streg lh.sphere.left_right > > rh.sphere.left_right --trg rh.your.label > > > > where the left_right files are in fsaverage/surf > > > > > > My fsaverage doesn't seem to have those registrations (we're still on > > 5.3) - I have lh.sphere, lh.sphere.reg, and lh.sphere.reg.avg but > > nothing with the .left_right suffix. > > > > -a > > -- > > Abigail L. Noyce, Ph.D. > > Psychological & Brain Sciences > > Boston University > > > > ano...@bu.edu <mailto:ano...@bu.edu> > > 617-440-3640 <(617)%20440-3640> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 9 > Date: Tue, 3 Apr 2018 16:01:45 -0400 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Surface label to volume and then back to > surface > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1600e55a-3097-8455-cb9a-7725ce6e3...@mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252"; format=flowed > > Hi David, I've tried to answer your questions below. > > doug > > > On 03/30/2018 01:48 PM, David Beeler wrote: > > Hi all, > > Sorry in advance, this is a bit of an annoying one! > > > > I am trying to use freesurfer's automatically generated MT label as a > > parcel to constrain activity measured during a functional MT > > localizer. I am currently doing my analysis in the volume and I'd like > > to transform the MT surface label into the subject's volume functional > > space (i.e. the same space as the sig.nii.gz for a particular > > contrast), take the voxels in sig.nii.gz that are within the MT label, > > and project them back onto the surface (preferably to be viewed as an > > overlay with freeview). I will eventually run the analysis on the > > surface as well (making this much less roundabout, but I also use > > volume parcels so understanding how to correctly go between the volume > > and surface is important to me). > > > > In my pipeline I start off by running preproc-sess, then I register > > and transform my preprocessed functional data (fmcpr.nii.gz) to the > > subject's anatomical (without upsampling). After doing mkanalysis and > > mkcontrast, I run selxavg on this volume. So the functional data is > > aligned with the anatomical, but still has low res dimensions. > > > > If it's not too much to ask, would it be possible to provide the > > specific commands to do all these transformations properly? I'll > > provide some of the commands I've tried below so you can see where I'm > > going wrong: > > > > First I want to transform the MT label to the functional volume. I've > > tried: > > > > mri_label2vol --subject $SUBJID --label > > $SUBJECTS_DIR/$SUBJID/label/rh.MT.label --o > > $OUTPUTDIR/rh.MT.volume.anat.nii.gz --temp > > $SUBJECTS_DIR/$SUBJID/mri/orig.mgz --identity --fill-ribbon --hemi rh > > > > ...which I would expect to put the label in high resolution anatomical > > volume space (orig.mgz), but it doesn't fill the graymatter ribbon > > nicely at all. > I? would have expected this to work. Can you send a pic? I just ran it > myself, and it seemed to do ok. > > > > I then use mri_vol2vol to transform to functional/sig.nii.gz space (I > > could also just downsample with mri_convert since I've already aligned > > my sig.nii.gz to my anatomical, this gives me the same result). I am > > using regheader here, is this okay? > > > > mri_vol2vol --regheader --mov $OUTPUTDIR.rh.MT.volume.anat.nii.gz > > --targ meanfunc.nii.gz --o rh.MT.volume.func.nii.gz --nearest > > > > ...and this works pretty well, but it's a little sparse so I may need > > to dilate it with mri_morphology. I think this step is fine. > Why do this extra step? I think you could do it with a single call to > mri_label2vol using --regheader and specifying the func template. Why > are you using --regheader here instead of the register.dof6.lta? > > > > Next I use matlab to take the voxels in sig.nii.gz that are also in > > rh.MT.volume.func.nii.gz and I save that as a new volume, say > > constrainedsig.nii.gz. > You can do this with mri_mask sig.nii.gz rh.MT.volume.func.nii.gz > constrainedsig.nii.gz > > Now I want to transform constrainedsig.nii.gz to the surface. I have > > tried going directly using the register.dof6.lta generated from > > preproc-sess: > > > > mri_vol2surf --mov constrainedsig.nii.gz --reg register.dof6.lta > > --projfrac 0.5 --interp nearest --hemi rh --o > > $OUTPUTDIR/constrainedsig_surface.nii.gz > This should have worked. Try doing directly on the rh.MT.volume.func.nii.gz > > > > ... and this is in the right area, but its shape doesn't match the > > shape of the original label. So I've also tried backtracking and doing > > another vol2vol and then vol2surf with regheader: > > > > mri_vol2vol --regheader --mov constrainedsig.nii.gz --targ > > $SUBJECTS_DIR/$SUBJID/mri/orig.mgz --o > > $OUTPUTDIR/constainedsig_anatvolume.nii.gz > > > > mri_vol2surf --mov constrainedsig_anatvolume.nii.gz --hemi rh > > --regheader S02 --o $OUTPUTDIR/constrainedsig_anatsurface > > > > ...and while this ends up in the right place, it is really patchy > > (looking kind of like twisty zebra stripes). Seems to me like it has > > the wrong dimensions or something, but mri_info says it's the same > > dimensions as the volume I originally created with mri_label2vol. > > > > Any help is much appreciated, thanks! > > David > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > Message: 10 > Date: Tue, 3 Apr 2018 22:48:12 +0000 > From: Dave Yas <davema...@hotmail.com> > Subject: Re: [Freesurfer] [Freesurfer/FSFAST] > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > bn7pr06mb414709f8be4b63bdbba8cf21b3...@bn7pr06mb4147.namprd06.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > Yes, the file exists! > > Here is the full output: > > > > -------------------------------------------------------------- > preproc-sess logfile is log/preproc-sess.sess01.log > -------------------------------------------------------------- > $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ > Davey > setenv FREESURFER_HOME /Applications/freesurfer > setenv SUBJECTS_DIR /Applications/freesurfer/subjects > Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 > 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 > /Users/Studies/Directory/Study_Directory > /Applications/freesurfer/fsfast/bin/preproc-sess > -fsd bold -per-run -s sess01 -fwhm 5 > Tue Apr 3 10:11:25 JST 2018 > instem f > mc 1 f fmcpr > stc 0 fmcpr > sm 1 fmcpr fmcpr.sm5 > mask 1 brain > sess01 Template ----------------------------- > mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory -fsd > bold -update > > > > Session: /Users/Studies/Directory/Study_Directory/sess01 ---------------- > Tue Apr 3 10:11:25 JST 2018 > Detected input format at nii > /Users/Studies/Directory/Study_Directory > mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii > /Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz > --frame 0 > mri_convert /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii > /Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz > --frame 0 > INFO: using NIfTI-1 qform > > Error: niiRead(): error reading from > /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from > /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii... > > > After that nothing happens.. > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve < > dgr...@mgh.harvard.edu> > Sent: Tuesday, April 3, 2018 1:17 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] [Freesurfer/FSFAST] > > > does that file exist? CAn you send the full terminal output? > > On 4/2/18 9:53 PM, Dave Yas wrote: > > Hi, > > > I am running preproc-sess on one subject. > > I got the following error after running preproc-sess: > > > Error: niiRead(): error reading from > /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii > > My PWD: /Users/Studies/Directory/Study_Directory > > My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects > > My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5 > > My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & > subjectname.text/001/f.nii & paradigm file (.par) > > > ~/002/f.nii & paradigm file > > > > ~/003/f.nii & paradigm file > > > Any help on the above? > > I searched the previous mailing list and found someone who had the same > problem but didn't reach a solution! > > > > Thank you in advance, > > > DWY > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180403/d2042029/attachment-0001.html > > ------------------------------ > > Message: 11 > Date: Tue, 3 Apr 2018 19:42:22 -0400 > From: Douglas Greve <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] [Freesurfer/FSFAST] > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <f5ce234c-b076-6328-0b33-eef5cb5bb...@mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Is the disk full? > > > On 4/3/18 6:48 PM, Dave Yas wrote: > > > > Yes, the file exists! > > > > Here is the full output: > > > > > > > > -------------------------------------------------------------- > > preproc-sess logfile is log/preproc-sess.sess01.log > > -------------------------------------------------------------- > > $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ > > Davey > > setenv FREESURFER_HOME /Applications/freesurfer > > setenv SUBJECTS_DIR /Applications/freesurfer/subjects > > Darwin DWYs-Mac-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr > > 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 > > /Users/Studies/Directory/Study_Directory > > /Applications/freesurfer/fsfast/bin/preproc-sess > > -fsd bold -per-run -s sess01 -fwhm 5 > > Tue Apr? 3 10:11:25 JST 2018 > > instem ? f > > mc ? 1 ? ? f fmcpr > > stc? 0 ? ? fmcpr > > sm ? 1 fmcpr fmcpr.sm5 > > mask 1 ? brain > > sess01 Template ----------------------------- > > mktemplate-sess -s sess01 -d /Users/Studies/Directory/Study_Directory > > -fsd bold -update > > > > > > Session: /Users/Studies/Directory/Study_Directory/sess01 ---------------- > > Tue Apr? 3 10:11:25 JST 2018 > > Detected input format at nii > > /Users/Studies/Directory/Study_Directory > > mri_convert > > /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii > > /Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz > > --frame 0 > > mri_convert > > /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii > > /Users/Studies/Directory/Study_Directory/sess01/bold/template.nii.gz > > --frame 0 > > INFO: using NIfTI-1 qform > > > > Error: niiRead(): error reading from > > /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > > > reading from > > /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii... > > > > > > After that nothing happens.. > > > > > > ------------------------------------------------------------------------ > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve > > <dgr...@mgh.harvard.edu> > > *Sent:* Tuesday, April 3, 2018 1:17 PM > > *To:* freesurfer@nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] [Freesurfer/FSFAST] > > > > does that file exist? CAn you send the full terminal output? > > > > > > On 4/2/18 9:53 PM, Dave Yas wrote: > >> > >> Hi, > >> > >> > >> I am running preproc-sess on one subject. > >> > >> I got the following error after running preproc-sess: > >> > >> > >> Error: niiRead(): error reading from > >> /Users/Studies/Directory/Study_Directory/sess01/bold/001/f.nii > >> > >> My PWD: /Users/Studies/Directory/Study_Directory > >> > >> My echo $SUBJECTS_DIR: /Applications/freesurfer/subjects > >> > >> My command: preproc-sess -fsd bold -per-run -s -sess01 -fwhm 5 > >> > >> My directory hierarchy: ~/Directory/Study_Directory/sess01/bold & > >> subjectname.text/001/f.nii& paradigm file (.par) > >> ?~/002/f.nii & paradigm file > >> > >> ?? ~/003/f.nii & paradigm file > >> > >> > >> Any help on the above? > >> > >> I searched the previous mailing list and found someone who had the > >> same problem but didn't reach a solution! > >> > >> > >> > >> Thank you in advance, > >> > >> > >> DWY > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180403/2c26024c/attachment-0001.html > > ------------------------------ > > Message: 12 > Date: Tue, 3 Apr 2018 23:47:36 +0000 > From: Dave Yas <davema...@hotmail.com> > Subject: Re: [Freesurfer] [Freesurfer/FSFAST] > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <BN7PR06MB414705091E095059CB94053BB3A50@BN7PR06MB4147.n > <bn7pr06mb414705091e095059cb94053bb3...@bn7pr06mb4147.namprd06.prod.outlook.com> -- Abigail L. Noyce, Ph.D. Psychological & Brain Sciences Boston University ano...@bu.edu 617-440-3640
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