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/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@bu.edu <mailto:anoyce@bu.edu>
> 617-440-3640
>
>
> _______________________________________________
> 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" <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
>
>
> _______________________________________________
> 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 <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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Message: 11
Date: Tue, 3 Apr 2018 19:42:22 -0400
From: Douglas Greve <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <f5ce234c-b076-6328-0b33-eef5cb5bb979@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-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
>>
>>
>>
>>
>> _______________________________________________
>> 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

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Message: 12
Date: Tue, 3 Apr 2018 23:47:36 +0000
From: Dave Yas <davemania@hotmail.com>
Subject: Re: [Freesurfer] [Freesurfer/FSFAST]
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BN7PR06MB414705091E095059CB94053BB3A50@BN7PR06MB4147.n