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@mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 170, Issue 1 To: freesurfer@nmr.mgh.harvard.edu Message-ID: 39459d44-cf44-6a53-1f0f-2eab5c471bf3@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@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/surfMy 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@bu.edu mailto:anoyce@bu.edu 617-440-3640 <(617)%20440-3640>
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Message: 9 Date: Tue, 3 Apr 2018 16:01:45 -0400 From: "Douglas N. Greve" dgreve@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-7725ce6e322c@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
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Message: 10 Date: Tue, 3 Apr 2018 22:48:12 +0000 From: Dave Yas davemania@hotmail.com Subject: Re: [Freesurfer] [Freesurfer/FSFAST] To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: < BN7PR06MB414709F8BE4B63BDBBA8CF21B3A50@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@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve < dgreve@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
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