Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

Unsubscribing
by Barnali Basu 04 Apr '18

04 Apr '18

Hi , I have not used this for years, could you please take me off the mailing list? Thank you Barnali Basu Cell : 425 638 2936 Home: 206 257 0174

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which dev version for amygdala segmentation
by Anik Dar 04 Apr '18

04 Apr '18

Hi All, How do I download reqd. files / FS developmental version to run hippocampal/amygdala pipeline as described in the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… I tried downloading the el capitan version of the development version of freesurfer from the https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall and I cant find any code segmentHA_T1.sh Can anyone help, Thanks Ani

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Full-Time Research Assistant Position in Clinical Neuroscience at Ohio State University
by Herring, Elizabeth J. 04 Apr '18

04 Apr '18

Posted on behalf of Dr. Ruchika Prakash: Research Assistant Position Clinical Neuroscience Laboratory Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position, Clinical Neuroscience Laboratory<http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html> of Dr. Ruchika Prakash at the Ohio State University to assist in the general coordination and conduct of research in the Clinical Neuroscience Laboratory, including the administration of tests and/or questionnaires and the compilation of results; facilitate recruitment efforts between the laboratory and community partners for human subject payments; conduct neuropsychological assessment sessions with clinical populations; assist with data reduction and analyses, specifically analyses of neuroimaging data using openly-available software like FSL, AFNI, or SPM and programming experience in either UNIX or MATLAB; supervise undergraduate research assistants. Desired qualifications include: Bachelor's degree in a psychology or neuroscience; programming experience in either UNIX or MATLAB, as well as experience in neuroimaging data analyses; knowledge of software package, such as FSL, AFNI, or SPM. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com, under job listing #437275 and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. Ruchika Prakash at prakash.30(a)osu.edu Lab Website: http://freud.psy.ohio-state.edu/lab/CNL/The_Lab.html The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.

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extracting morphometric values from co-ordinates
by Emmanuel Nwosu 04 Apr '18

04 Apr '18

Dear FreeSurfer Experts, Am wondering if there is a way to extract morphometry (cortical thickness, area, etc) values from a specific co-ordinate (talaraich, MNI, etc) of interest. Any help with this will be appreciated. Kind regards Emmanuel

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Re: [Freesurfer] mirroring fsaverage labels between hemispheres
by Abigail Noyce 04 Apr '18

04 Apr '18

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" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 170, Issue 1 > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <39459d44-cf44-6a53-1f0f-2eab5c471bf3(a)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 <dgreve(a)mgh.harvard.edu > > <mailto:dgreve@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 > > > > anoyce(a)bu.edu <mailto:anoyce@bu.edu> > > 617-440-3640 <(617)%20440-3640> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Surface label to volume and then back to > surface > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1600e55a-3097-8455-cb9a-7725ce6e322c(a)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(a)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 <davemania(a)hotmail.com> > Subject: Re: [Freesurfer] [Freesurfer/FSFAST] > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > < > BN7PR06MB414709F8BE4B63BDBBA8CF21B3A50(a)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-bounces(a)nmr.mgh.harvard.edu < > freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas Greve < > dgreve(a)mgh.harvard.edu> > Sent: Tuesday, April 3, 2018 1:17 PM > To: freesurfer(a)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(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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FSGD file error
by Dijkshoorn, A.B.C. (Aicha) 04 Apr '18

04 Apr '18

Dear free surfer developers, When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underlying languages, since it appears to occur both when I create a plain txt file or when I adjust the tutorials gender_age.fsgd and adjust the values of the covariates. I have tried tons of things to fix the problem, but i can't seem to figure it out... Do you by any chance have an idea on how I can fix this? error (in bash): ERROR: matrix is ill-conditioned or badly scaled, condno = 15250.9 command line: mri_glmfit --y lh.CB10.thickness.20.mgh --fsgd doesnotworkretestCB10.fsgd doss --C con-hem.mtx --surf fsaverage lh --cortex --glmdir lh.CB10.20.thickness.glmdir Thank you in advance for your time and effort! Kind regards, A. Dijkshoorn

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[Freesurfer/FSFAST]
by Dave Yas 03 Apr '18

03 Apr '18

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

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Surface label to volume and then back to surface
by David Beeler 03 Apr '18

03 Apr '18

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 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. 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. 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 ... 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

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Re: [Freesurfer] Freesurfer Digest, Vol 170, Issue 1
by Abigail Noyce 03 Apr '18

03 Apr '18

> Date: Mon, 2 Apr 2018 14:55:47 -0400 > From: Douglas Greve <dgreve(a)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 anoyce(a)bu.edu 617-440-3640

2 1

Percent Signal Change
by Sarah Cole 03 Apr '18

03 Apr '18

Hi, Could someone please let me know how to get the percent signal change for raw signal intensity? I think the cespct.nii.gz gives me the contrast as %. However, I am not sure about dividing h.nii and h-offset.nii. What are they? Thank you

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Freesurfer April 2018