Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

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

2 2

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 > >

1 0

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

3 5

[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

2 9

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

2 1

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

3 7

Hemodynamic Lag Shift
by Sarah Cole 03 Apr '18

03 Apr '18

Hi Doug, I have a block design experiment. After analyzing the data and plotting the response magnitude across the TRs, we see that there is a systematic lag in the response. For example, in a 16s block (TR=2s), at TR-1 and TR-2 the response goes down and then starts rising from TR-3. This is consistent across the subjects and blocks. We used to shift our raw data by 2 TRs when we were using SPM. How can we do this in FreeSurfer? Thank you, Sarah

3 5

Re: [Freesurfer] Freesurfer Digest, Vol 169, Issue 41
by Darko Komnenić 03 Apr '18

03 Apr '18

Hi Bruce, I attached the recon-all.log! Thanks in advance for taking a look! Darko Message: 3 Date: Sat, 31 Mar 2018 06:47:12 -0400 From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_watershed Error: indices out of bounds To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <23B23889-C042-4A04-9316-4C8ED5468428(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8 Can you send us the recon-all.log? > On Mar 30, 2018, at 11:32 AM, Darko Komneni? <komnenicd(a)gmail.com> wrote: > > Dear experts, > while running recon-all on FreeSurfer 5.1.0 I encountered the following error: > mri_watershed Error: indices out of bounds > > I searched the email archive and found this thread: > https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… > My problem seems identical to the one described by initial poster. > The suggestion was to try the following command: > set mdir=$SUBJECTS_DIR/$subject/mri > mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz > $mir/nu.mgz > > When I tried it, the message I got was: > mri_add_xform_to_header: could not open source file /nu.mgz > No such file or directory > And indeed such file does not exist in the mri subfolder of my > current subject's folder. > > Any further suggestions on how to fix this? Like the person asking > originally, this is the only participant where it happened, for > others, recon-all finished without error and all the images were > acquired in the same scanner. > Thanks in advance! > Best, > Darko > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

1 0

Fwd: Learning Workshop in Bloomington IN (fwd)
by Bruce Fischl 03 Apr '18

03 Apr '18

FYI ---------- Forwarded message ---------- Date: Tue, 3 Apr 2018 11:14:38 -0400 From: Satrajit Ghosh <satra(a)mit.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, "Jog, Amod" <AJOG(a)mgh.harvard.edu> Subject: Fwd: Learning Workshop in Bloomington IN hi, this may be of interest. please forward. cheers, satra -- satrajit ghosh | satra.cogitatum.org principal research scientist | mibr @ m i t assistant professor of otolaryngology @ harvard medical school faculty member @ speech and hearing bioscience and technology director, data models and integration | repronim: center for reproducible neuroimaging computation ---------- Forwarded message ---------- From: Franco Pestilli <frakkopesto(a)gmail.com> Date: Tue, Apr 3, 2018 at 10:51 AM Subject: Learning Workshop in Bloomington IN To: Satrajit Ghosh <satrajit.ghosh(a)gmail.com> Dear Satra We are organizing a learning workshop in Bloomington Indiana May 14-15: http://www.indiana.edu/~earbmc/LIHAM/ Would you mind spreading the word please? We have travel scholarships for talented trainees. Best regards, Franco Franco Pestilli, PhD Assistant Professor in Psychology, Neuroscience and Cognitive Science Adjunct Professor in Engineering, Computer Science, and Optometry Indiana Network Science Institute 𝞇 Indiana University, Bloomington francopestilli.com | brainlife.io franpest(a)indiana.edu | +1 (812) 856 9967

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