Re: [Freesurfer] parcellation-based connectome viewing in freeview.

[Octavian Lie]

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Thank you, this is very helpful. Octavian

On Wed, Jan 13, 2021 at 9:19 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> this might be something you can do in matlab with the function below
> (found in $FREESURFER_HOME/matlab)
>
>
> function surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile)
> % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile)
> %
> % Example:
> % I have three annotations
> %   annotnames = strvcat('superiortemporal','insula','postcentral');
> % with matchine values
> %   annotvals = [1.1 2.2 3.7];
> % I want to create a surface overlay with all the vertices in a
> % given annotation having its corresponding value (ie, all vertices
> % in superior temporal gyrus being a value of 1.1, etc)
> %
> % Run these commands in matlab
> % annotnames = strvcat('superiortemporal','insula','postcentral');
> % annotvals = [1.1 2.2 3.7];
> % annotfile = '~/subjects/fsaverage/label/lh.aparc.annot';
> % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile);
> % clear mri
> % mri.vol = surfoverlay;
> % MRIwrite(mri,'vals.mgh');
> %
> % Run this command from a linux shell:
> %   tksurferfv fsaverage lh inflated -aparc -ov vals.mgh -fminmax .01 1
> %
>
>
>
> On 1/6/2021 10:11 AM, Octavian Lie wrote:
>
> External Email - Use Caution
> Dear All,
>
> I have a destrieux-based connectome weight matrix, and wanted to see the
> edge weights between parcels as color-coded activations in freeview,
> something like the attached fig. I think that would be possible, if able to
> transform the weights txt file (symmetric matrix, it could be a .dat file)
> into an .mgh file to overlay it in freeview. Please let me know if it can
> be done, and how to, or there is another way.
>
> Thank you,
> Octavian
>
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Re: [Freesurfer] write .annot files

[Octavian Lie]

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Thank you, Bruce. Just to exhaust the annot issue. I assume that the labels
(parcel names) are not embedded in .annot or aparc+aseg.mgz per se, but
they are read from the LUT table by matching annot vertex indices to col 1
in the LUT. Is there any .m file that can do that? If not, I can write one,
but wanted to check, thank you.
Octavian

On Fri, Jan 8, 2021 at 11:03 AM Fischl, Bruce 
wrote:

> Alas there is not – there are large parts of the cortex that have not  yet
> been mapped for microstructural boundaries
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Octavian Lie
> *Sent:* Friday, January 8, 2021 11:59 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] write .annot files
>
>
>
> *External Email - Use Caution*
>
> Thank you, Bruce, as always. The BA_exvivo.thresh.annot does not annotate
> all the vertices, see attached BA.png. Is there a complete Brodmann map
> like in the atlas image? Thank you, Octavian
>
>
>
> On Fri, Jan 8, 2021 at 10:37 AM Fischl, Bruce 
> wrote:
>
> Hi Octavian
>
>
>
>1. Yes, there is a write_annotation.m that you can use.
>2. We output an annot of the max probability labels at each point I
>think called BA_exvivo.thresh.annot
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Octavian Lie
> *Sent:* Friday, January 8, 2021 11:26 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] write .annot files
>
>
>
> *External Email - Use Caution*
>
> Dear All,
>
>
>
> These are probably rookie questions.
>
> 1. I can read an .annot file with read_annotation.m, is there a way to
> write one? (for example read it to matlab, modify, and save, or create a
> combined (lh+rh) aparc.annot file etc.
>
>
>
> 2. On the same line, how one combines all the Brodmann labels into a
> Brodmann parcellation, if not done already..
>
> Thank you,
>
> Octavian
>
>
>
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[Freesurfer] write .annot files

[Octavian Lie]

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Dear All,

These are probably rookie questions.
1. I can read an .annot file with read_annotation.m, is there a way to
write one? (for example read it to matlab, modify, and save, or create a
combined (lh+rh) aparc.annot file etc.

2. On the same line, how one combines all the Brodmann labels into a
Brodmann parcellation, if not done already..
Thank you,
Octavian
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Re: [Freesurfer] -T2pial after white matter edits

[Octavian Lie]

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Dear Doug
Just to be clear

I  ran the 1st process on subject x with

recon-all -s x -T2 volT2.nii  -T2pial

It still needed wm edits. On rerun, can I just do

recon-all -s x  autorecon2-wm -autorecon3

or I need to reuse the T2 for best results

recon-all -s x  autorecon2-wm -autorecon3  -T2 volT2.nii  -T2pial

If so, can I obtain similar results with mri/orig/T2 raw.mgz instead of the
volT2.nii input?
Thanks,
OL

On Mon, May 4, 2020 at 10:49 AM Douglas N. Greve 
wrote:

> Sorry, our interface is a little bit confusing on this. Use -T2 to specify
> the T2 volume (eg, -T2 /path/to/T2.mgz). To apply the T2 to the pial use
> -T2pial (without any arguments)
>
> On 5/2/2020 7:55 PM, Octavian Lie wrote:
>
> External Email - Use Caution
> Dear All,
>
> I ran recon-all on the 1st run using the -T2pial flag. After wm.mgz edits,
> when running
> recon-all autorecon2-wm -autorecon3 -T2pial volT2.mgz
> it throws an error ~ 'flag volT2.mgz not recognized'. When reruning
> recon-all as above, do we need to include the T2pial flag to make use of
> the t2 pial information? If not, is the previous T2pial output used to
> regenerate the pia?
> Thank you,
> OL
>
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[Freesurfer] -T2pial after white matter edits

[Octavian Lie]

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Dear All,

I ran recon-all on the 1st run using the -T2pial flag. After wm.mgz edits,
when running
recon-all autorecon2-wm -autorecon3 -T2pial volT2.mgz
it throws an error ~ 'flag volT2.mgz not recognized'. When reruning
recon-all as above, do we need to include the T2pial flag to make use of
the t2 pial information? If not, is the previous T2pial output used to
regenerate the pia?
Thank you,
OL
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Re: [Freesurfer] bbregister & mri_convert

[Octavian Lie]

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Thank you.  Can you please clarify, documentation for mri_convert states
default for resampling is -interpolate, does this mean trilinear? Also,
which method is preferable for bbregister (I am applying it for
intrasubject uni and multimodal registration), trilinear or cubic
interpolation? I assume trilinear if that is the default, but cubic is
listed in recon-all dev table in the -T2pial (multimodal) step, see below.
Thank you again, Octavian

bbregister --s  --mov mri/orig/T2raw.mgz --lta
mri/transforms/T2raw.lta --init-fsl --T2

transforms/T2raw.lta

orig/T2raw.mgz

mri_convert -odt short -at mri/transforms/T2raw.lta -rt *cubic* -ns 1 -rl
mri/orig.mgz mri/orig/T2raw.mgz mri/T2.prenorm.mgz

On Thu, Apr 30, 2020 at 1:16 PM Douglas N. Greve 
wrote:

> It will but, it will always be resampled with trilinear interpolation.
>
> On 4/30/2020 12:55 PM, Octavian Lie wrote:
>
> External Email - Use Caution
>
> Dear All,
>
> I have seen bbregister command lines using --o option to get the final
> output (say a .nii vol), and others where bbregister is used to get an lta
> transform, which is used in a follow-up step (mri_convert with -ns 1 (no
> scale), and -rl orig.mgz (reslice-like)
>
>
> Are these options equivalent? meaning
> when using bbregister with '--o x.nii' option, is the output volume x.nii
> resliced to orig.mgz, and without rescale?
>
> Thanks,
> Octavian
>
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[Freesurfer] bbregister & mri_convert

[Octavian Lie]

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Dear All,

I have seen bbregister command lines using --o option to get the final
output (say a .nii vol), and others where bbregister is used to get an lta
transform, which is used in a follow-up step (mri_convert with -ns 1 (no
scale), and -rl orig.mgz (reslice-like)


Are these options equivalent? meaning
when using bbregister with '--o x.nii' option, is the output volume x.nii
resliced to orig.mgz, and without rescale?

Thanks,
Octavian
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[Freesurfer] kill recon-all programatically/remotely

[Octavian Lie]

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Dear All,

Is there a way to kill a  recon-all run on linux via ssh/putty. Ctrl+C is
not working, obviously, and it is not easy to figure out which process
encodes the recon-all runs with commands such as ps aux, top etc. One gross
way may be removing the subject directory all together midway, but not sure
how this affects FS, subsequent runs
Thank you,
Octavian
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Re: [Freesurfer] registrations

[Octavian Lie]

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Dear Bruce & All,

Sure, I wanted some advice from the greats before registering pre and
posteresection (intrasubject) scans.
I tried both registrations on several patient data, bbregister clearly
superior to mri_robust_register (used with orig/mgz) for both
postresection T1 or T2 registration to FS output, even when using a
mask for the resection volume with the latter.
The best results were using one hemisphere option (the
healthy/nonresected one), and the default or init-fsl for
initialization (init-spm and init-rr failed often), smth like
bbregister --s subj --mov T1postop.nii --lta register_hemiR.lta --o
T1bbr_hemiR_fsl.nii --t1 --rh-only --init-fsl

My last question relates to creating a binary mask from pial surfaces,
but to include mesial temporal structures (amygdala, hippocampus). I
tried the following, but the mris_fill process is killed (OOM) after I
upgraded to ubuntu 18.04. Is there another, more straightforward
solution for the mask?
Thank you,
Octavian

mris_fill -c -r 1 surf/rh.pial mri/rh.pial.filled.mgz & \
mris_fill -c -r 1 surf/lh.pial mri/lh.pial.filled.mgz & \
mri_concat --combine --i mri/rh.pial.filled.mgz --i
mri/lh.pial.filled.mgz --o mri/pial.filled.mgz
cd ./mri ; \
mri_binarize --i aseg.mgz --match 5 --match 9 --match 10 --match 14
--match 17 --match 18 --match 19\
 --match 25 --match 31 --match 44 --match 48 --match 49 --match 53
--match 54 --match 55 --match 57\
 --match 63 --match 86 --match 96 --match 97 --match 105 --match 106
--match 114 --match 115\
 --match 195 --match 199 --match 203 --match 204 --match 205 --match
216 --match 222 --match 225\
 --match 507 --match 557 --match 1200 --match 1201 --match 1205
--match 1206 --match 2200 --match 2201\
 --match 2205 --match 2206 --o hippoamy.mask.mgz & \
fscalc pial.filled.mgz add hippoamy.mask.mgz -o epimask.mgz







On Sun, Feb 23, 2020 at 8:51 PM Bruce Fischl  wrote:
>
> Hi Octavian
>
> 1. Not sure - you should try them. If you have reasonable surfaces I
> think bbreg lets you specify masks to ignore, which should be giant help
> in this scenario. On the other hand, mri_robust_register does this
> automatically. They are both relatively fast so why not try and see?
>
> 2. Same answer as before. mri_robust_register has flags to tell it to use
> an inter-modal similarity function, but you can also tell bbregister it is
> a T2 and it should do a good job (and implicitly register to the T1 since
> it is already aligned with the surface).
>
> 3. I'm not sure what you mean - can you explain further?
>
> cheers
> Bruce
>
>
>
> On Sun,
> 23 Feb 2020, Octavian Lie wrote:
>
> >External Email - Use Caution
> >
> > Dear All,
> >
> > I need to register:
> > 1. T1.mgz to a T1 postresection volume (no contrast), with large
> > resection. Which one should I use, mri_robust_register, or bbregister,
> > if the latter, which is the better initiator (nmi, spm, fsl)?
> >
> > 2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space
> > recon-all flag), which FS registration tool should I use?
> >
> > 3. I then need to mask the coregistered T1 postresection with a T1.mgz mask.
> >
> > I would appreciate commands (either names, or full command lines),
> > please advise.
> >
> > Thank you,
> > Octavian
> >
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> >
> >
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Re: [Freesurfer] registrations

[Octavian Lie]

External Email - Use Caution

Dear Bruce, thank you for your replies.

I planned using this line for intrasubject pre to postop
(postresection) MRI T1 registration
1. with mri_robust_register:

mri_robust_register --mov postop.mgz --dst preop.mgz --lta
posttopre.lta --mapmov posttopre.mgz --weights posttopre-weights.mgz
--iscale --satit -- maskmov itksnap_rezvol.nii

2.  with bbregister
bbregister --s sbj --mov postop.mgz --init-fsl --reg register.lta --o
posttopre.mgz --t1

Here are follow-up questions and clarifications:
1. With bb register, I do not see an optional flag to accommodate a
custom mask volume, such as a mask of the resection volume; if this is
true, then one is not required, please advise
2. If one wants to try mri_robust_register for pre to postop MRI
alignment, which pre volume from the FS recon pipeline would be
indicated for best results? T1.mgz, brain.mgz, or another?
3. With bbregister, which of the several init options (coreg, header,
spm, or fsl) are recommended (I have all external packages installed,
so that is not an issue), or there is no rule?
4. With mri_robust_register, since the vol of resection is small
(sublobar, at most lobar) in size, does a mask of the resection volume
for 6 DOF registration improve registration? Or the mask refers more
to more partial volumes such as slices, or hemi alignment, as in
example 3 here (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_register)?
5. A very rookie question: if one has to use a resection volume mask,
do the inside-resection voxels have to be 1, and all outside 0, or the
other way around?
6. I then need to mask the coregistered postop volume (posttopre.mgz)
with a mask derived from FS preop pipeline, to include all cerebrum
(ribbon.mgz) (no cerebellum) but also mesial temporal structures
hippocampus/amygdala etc; is there such a mask in the recon pipeline,
or it has to be constructed?
Thank you,
OL

On Sun, Feb 23, 2020 at 8:51 PM Bruce Fischl  wrote:
>
> Hi Octavian
>
> 1. Not sure - you should try them. If you have reasonable surfaces I
> think bbreg lets you specify masks to ignore, which should be giant help
> in this scenario. On the other hand, mri_robust_register does this
> automatically. They are both relatively fast so why not try and see?
>
> 2. Same answer as before. mri_robust_register has flags to tell it to use
> an inter-modal similarity function, but you can also tell bbregister it is
> a T2 and it should do a good job (and implicitly register to the T1 since
> it is already aligned with the surface).
>
> 3. I'm not sure what you mean - can you explain further?
>
> cheers
> Bruce
>
>
>
> On Sun,
> 23 Feb 2020, Octavian Lie wrote:
>
> >External Email - Use Caution
> >
> > Dear All,
> >
> > I need to register:
> > 1. T1.mgz to a T1 postresection volume (no contrast), with large
> > resection. Which one should I use, mri_robust_register, or bbregister,
> > if the latter, which is the better initiator (nmi, spm, fsl)?
> >
> > 2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space
> > recon-all flag), which FS registration tool should I use?
> >
> > 3. I then need to mask the coregistered T1 postresection with a T1.mgz mask.
> >
> > I would appreciate commands (either names, or full command lines),
> > please advise.
> >
> > Thank you,
> > Octavian
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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> >
> >
> >
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[Freesurfer] registrations

[Octavian Lie]

External Email - Use Caution

Dear All,

I need to register:
1. T1.mgz to a T1 postresection volume (no contrast), with large
resection. Which one should I use, mri_robust_register, or bbregister,
if the latter, which is the better initiator (nmi, spm, fsl)?

2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space
recon-all flag), which FS registration tool should I use?

3. I then need to mask the coregistered T1 postresection with a T1.mgz mask.

I would appreciate commands (either names, or full command lines),
please advise.

Thank you,
Octavian

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Re: [Freesurfer] freeview slow/choppy

[Octavian Lie]

External Email - Use Caution

Hello Andrew,
I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Thank you,
Octavian

On Mon, Feb 10, 2020 at 9:19 AM Hoopes, Andrew  wrote:
>
> Hi Octavian,
> what freesurfer version are you using?
> Andrew
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Octavian Lie 
> 
> Sent: Monday, February 10, 2020 9:32 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] freeview slow/choppy
>
> External Email - Use Caution
>
> Dear All, I recently changed from ubuntu 16.04 to 18.04 LTS, then
> reinstalled Freesurfer.
> As opposed to prior behavior, freeview image manipulation (mainly
> mouse-based rotations) are exceedingly choppy and slow. The screen
> briefly freezes after moving the mouse to rotate a volume, then jumps
> to the final volume position. Any thoughts?
> Thank you,
> Octavian
>
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[Freesurfer] freeview slow/choppy

[Octavian Lie]

External Email - Use Caution

Dear All, I recently changed from ubuntu 16.04 to 18.04 LTS, then
reinstalled Freesurfer.
As opposed to prior behavior, freeview image manipulation (mainly
mouse-based rotations) are exceedingly choppy and slow. The screen
briefly freezes after moving the mouse to rotate a volume, then jumps
to the final volume position. Any thoughts?
Thank you,
Octavian

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[Freesurfer] -usegpu vs -parallel in recon-all

[Octavian Lie]

Dear All,

With FS6, -parallel -openmp x can really speed things up. I inherited code
from prior versions using -usegpu flag for GPU/CUDA (not supported more
recently). Is the latter redundant or affecting in any way the -parallel
-openmp x performance, should we take it out, please advise.

Thank you,

Octavian
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Re: [Freesurfer] Fwd: wm edits not incorporated

[Octavian Lie]

Thank you,
this is very helpful.
Octavian

On Thu, Apr 13, 2017 at 12:19 PM, Antonin Skoch  wrote:

> Dear Octavian,
>
> the current philosophy with wm.mgz edits is not to directly affect voxel 
> values in original T1 image.
>
> The wm.mgz serves as starting point for the white surface estimation. The 
> ?h.white surface is estimated according gradient in voxel values in 
> brain.finalsurfs.mgz (which is, basically, preprocessed T1 image) using 
> basically preprocessed surfaces obtained from wm.mgz (?h.orig) as a starting 
> position where to search for intensity gradient.
> The editing of wm.mgz helps to find out the GM/WM itensity gradient and 
> properly place ?h.white there.
> Therefore, where there is insufficient GM/WM contrast, the wm.mgz cannot help 
> out. I think that there is no change in the behavior between v5.3 and v6.0 in 
> this aspect. I have seen many cases where wm.mgz edit does not help to 
> improve ?h.white surfaces in the data processed by v5.3.
>
> There is an -overlay option in mris_make_surfaces which explicitly modifies 
> voxel values in input image for mris_make_surfaces (brain.finalsurfs.mgz as 
> default in recon-all). However, this option only works for cases when wm.mgz 
> is extended, not deleted:
> In voxels which have value 255 in wm.mgz, it replaces current voxel value in 
> input image by desired value of white matter. This option is currently not 
> used in recon-all.
> I would opt for implementation of similar option for deletion of voxels in 
> wm.mgz: Where wm.mgz voxel values equal 1, to replace input image voxel 
> values by desired values of GRAY matter. This should force ?h.white to 
> directly follow edits of wm.mgz
>
> As for editing of 001.mgz, beware the pitfall with editing images with 
> mutually different geometry in FreeView I posted today:
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52729.html
>
> Antonin Skoch
>
>
> Dear All,
>
> Regarding wm.mgz edits not incorporated into wm surface, which seems to
> have been reported on by several of us with FS 6.00. I followed Antonin's
> idea of editing 001.mgz by switching wm-intensity voxels clearly not wm
> (mostly in the subtemporal regions, at times close to bright dural portions
> in the crown) to gm intensities and ran recon-all -all, and this time all
> was OK. So it seems that the problem is that on re-initializing during
> -autorecon2-wm rerun, the routine does not edit out high intensity voxels
> even if manually excluded in wm.mgz. This seems to be different to some
> extent with how FS 5.3 was reacting, although I did not look at this
> systematically. There may be a reason that manual editing is just part of
> the story during rerun and does not automatically override the recon
> stream, but I do not know it.
> Octavian
>
>
>
>
> -- Forwarded message --
> From: Octavian Lie 
> Date: Sun, Apr 2, 2017 at 7:59 PM
> Subject: wm edits not incorporated
> To: octavian lie 
>
>
>
> Dear Bruce,
>
> I just transferred subject r02.tar.gz.
>
> Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated
> on reruns using any of the
> recon-all -autorecon-wm -aitorecon3
> recon-all -autorecon2 -autorecon3
> recon-all -make all
>
> FOr example, the complete command line for  a rerun is
>
> recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02
> -parallel > output.txt &
>
>
> Here are some of the edited voxels which are not excluded from the wm on
> rerun:
>
>
> -40.14, -2.67, 116.29 coronal slice 132
> 12.73, -23.67, 126.16 coronal slice 171
> 14.05, 12.33, 11.61 coronal slice 147
>
>
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> addressed. If you believe this e-mail was sent to you in error and the
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[Freesurfer] Fwd: wm edits not incorporated

[Octavian Lie]

Dear All,

Regarding wm.mgz edits not incorporated into wm surface, which seems to
have been reported on by several of us with FS 6.00. I followed Antonin's
idea of editing 001.mgz by switching wm-intensity voxels clearly not wm
(mostly in the subtemporal regions, at times close to bright dural portions
in the crown) to gm intensities and ran recon-all -all, and this time all
was OK. So it seems that the problem is that on re-initializing during
-autorecon2-wm rerun, the routine does not edit out high intensity voxels
even if manually excluded in wm.mgz. This seems to be different to some
extent with how FS 5.3 was reacting, although I did not look at this
systematically. There may be a reason that manual editing is just part of
the story during rerun and does not automatically override the recon
stream, but I do not know it.
Octavian




-- Forwarded message --
From: Octavian Lie 
Date: Sun, Apr 2, 2017 at 7:59 PM
Subject: wm edits not incorporated
To: octavian lie 



Dear Bruce,

I just transferred subject r02.tar.gz.

Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated
on reruns using any of the
recon-all -autorecon-wm -aitorecon3
recon-all -autorecon2 -autorecon3
recon-all -make all

FOr example, the complete command line for  a rerun is

recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02
-parallel > output.txt &


Here are some of the edited voxels which are not excluded from the wm on
rerun:


-40.14, -2.67, 116.29 coronal slice 132
12.73, -23.67, 126.16 coronal slice 171
14.05, 12.33, 11.61 coronal slice 147


I mention this is not the only subject where I have this problem.
Thank you for your help.
Octavian
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Re: [Freesurfer] white matter edits not incorporated.

[Octavian Lie]

Dear All,

I wanted to know if there is any take on the issue of white matter edits
(specifically deleting unwanted voxels from wm.mgz). I sent a subject a
week ago for your review. It seems this is a problem that I had with
several scans, and by the message list, I am not the only one.
Recent users having the same issues have raised the possibility of editing
orig.mgz by replacing wm intensity with gm intensity in the troubled areas
as workaround to the wm.mgz issue.

Please let me know,

Thank you,

octavian




Dear Bruce,

I just transferred subject r02.tar.gz.

Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated
on reruns using any of the
recon-all -autorecon-wm -aitorecon3
recon-all -autorecon2 -autorecon3
recon-all -make all

FOr example, the complete command line for  a rerun is

recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02
-parallel > output.txt &


Here are some of the edited voxels which are not excluded from the wm on
rerun:


-40.14, -2.67, 116.29 coronal slice 132
12.73, -23.67, 126.16 coronal slice 171
14.05, 12.33, 11.61 coronal slice 147


I mention this is not the only subject where I have this problem.
Thank you for your help.
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Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

[Octavian Lie]

Hi there,

I have a similar problem not using longitudinal stream, just a routine
recon-all analyses, this with several processed subjects, Here is my
message sent several days ago.
Thanks,
Octavian.

Dear Bruce,

I just transferred subject r02.tar.gz.

Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated
on reruns using any of the
recon-all -autorecon-wm -aitorecon3
recon-all -autorecon2 -autorecon3
recon-all -make all

For example, the complete command line for  a rerun on this particular
subject is

recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02
-parallel > output.txt &


Here are some of the edited voxels which are not excluded from the wm on
rerun:


-40.14, -2.67, 116.29 coronal slice 132
12.73, -23.67, 126.16 coronal slice 171
14.05, 12.33, 11.61 coronal slice 147


I mention this is not the only subject where I have this problem.
Thank you for your help.
Octavian

On Tue, Apr 4, 2017 at 4:13 PM, David Semanek 
wrote:

> Thanks for looking into this. I have uploaded another two subject folders
> as dsemanek3.zip, this time from a single time point for the same subject
> having been run through the cross stream of recon-all, the one with “test”
> appended at the end has had white matter edits on sagittal slices 126-142.
>
>
>
> So, I have been able to get the surfaces to change in a single cross run
> as demonstrated in this upload. For this test, I did some edits that are
> typical on this dataset. Although the surfaces did change to reflect the
> edits, in a couple of places the surfaces did not change enough, and still
> encompassed space in the wm volume which had the white matter voxels
> removed.
>
>
>
> For the first pass through these data before I realized there was a
> potential problem, I had initially edited the cross folders for the
> subjects and then ran the base, expecting the edits to be transferred over,
> but they did not seem to be. So I am still left with two issues: 1)
> incomplete incorporation of cross edits on the cross folders, 2) so far
> being unable to find an intervention point which will change the surfaces
> in the long stream, I have edited the base and then ran the long folders
> and these were not carried over as demonstrated in my previous uploads.
>
>
>
> Thanks again,
>
>
>
> David P. Semanek, HCISPP
>
> Research Technician, Posner Lab
>
> Division of Child and Adolescent Psychiatry
>
> Columbia University Medical Center
>
> New York State Psychiatric Institute
>
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
>
> New York, NY 10032
>
> PH: (646) 774-5885
>
>
>
> IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended
> recipient.  It may contain confidential information which is legally
> privileged or otherwise protected by law.  If you received this e-mail in
> error or from someone who was not authorized to send it to you, you are
> strictly prohibited from reviewing, using, disseminating, distributing or
> copying the e-mail.  PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN
> E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM.  Thank you for your
> cooperation.
>
>
>
> *From: *Martin Reuter 
> *Date: *Tuesday, April 4, 2017 at 11:20 AM
> *To: *"freesurfer@nmr.mgh.harvard.edu" 
>
> *Subject: *Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in
> FS 5.3/6 Cross and Long Streams
>
>
>
> So the way to debug this is to test if we can replicate the problem of WM
> edits not taking effect in a regular cross sectional stream.
>
> If true this means that there is a bug to the way WM edits are considered
> in FS6.0. It is unlikely that we missed that, but can happen. Probably
> something else is going on here.
>
>
>
> For that it would be good to have a single time point (cross sectional
> step) with WM edits send over, so that Andrew can take a look at that.
>
>
>
> Best, Martin
>
>
>
>
>
> On 04/04/2017 05:03 PM, David Semanek wrote:
>
> I used –uselongbasewmedits only as a test to see if I could get some
> condition under which the wm edits would be taken into account when the
> surfaces were generated.
>
>
>
> I did not use that flag for the data I uploaded. The wm edits to base did
> not influence the base wm surfaces or the cross wm surfaces. The cross wm
> edits (not uploaded) did not influence cross, base, or long wm surfaces.
>
>
>
> I’ve found no condition under which wm edits have influenced the white
> matter surface in any of my data.
>
>
>
> Best,
>
>
>
> David P. Semanek, HCISPP
>
> Research Technician, Posner Lab
>
> Division of Child and Adolescent Psychiatry
>
> Columbia University Medical Center
>
> New York State Psychiatric Institute
>
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
>
> New York, NY 10032
>
> PH: (646) 774-5885
>
>
>
> IMPORTANT NOTICE:  This e-mail is meant only for the use of the intended
> recipient.  It may contain confidential information which is legally
> privileged or otherwise protected by law.  If you received this e-mail in
> error or from someon

Re: [Freesurfer] wm edits not incorporated

[Octavian Lie]

Dear Bruce,
>
> I just transferred subject r02.tar.gz.
>
> Again, wm.mgz edits (all deleted voxels, no additions) are not
> incorporated on reruns using any of the
> recon-all -autorecon-wm -aitorecon3
> recon-all -autorecon2 -autorecon3
> recon-all -make all
>
> For example, the complete command line for  a rerun on this particular
> subject is
>
> recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02
> -parallel > output.txt &
>
>
> Here are some of the edited voxels which are not excluded from the wm on
> rerun:
>
>
> -40.14, -2.67, 116.29 coronal slice 132
> 12.73, -23.67, 126.16 coronal slice 171
> 14.05, 12.33, 11.61 coronal slice 147
>
>
> I mention this is not the only subject where I have this problem.
> Thank you for your help.
> Octavian
>
>
>
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Re: [Freesurfer] wm edits not incorporated on recon-all rerun

[Octavian Lie]

Dear Bruce,

I am using the recon editing and all voxels removed are 1. If this is the
correct value for removed wm voxels during editing, Is there a way I could
send you a subject?
Thank you,

Octavian

On Sat, Apr 1, 2017 at 8:47 AM, Bruce Fischl 
wrote:

> Hi Octavian
>
> what tool are you using for the deletion of wm voxels? Make sure it is the
> "recon editing" tool in freeview or the equivalent. We do NOT set voxels to
> 0 when you erase - we set them to 1. This allows us to detect the erasure
> and preserve it during reprocessing.
>
> cheers
> Bruce
>
>
>
> On Fri, 31 Mar 2017, Octavian Lie wrote:
>
> Dear All,
>>
>> I am stuck. Several brains I segment need both wm and pial edits,
>> typically
>> deleting incorrectly incorporated voxels, such as dural voxels for pia,
>> and
>> basal temporal hyperintensity artifact or bright dural voxels included due
>> to partial volume effects for wm.
>>
>> I edited brainmask.mgz or brain.finalsurfs.manedit.mgz for pia, and wm.mgz
>> for wm. Rerunning recon-all led as expected to pial correction, however wm
>> edits did not end up in ?h.white, despite increasingly desperate efforts
>> and
>> commands:
>>
>> recon-all -autorecon2-wm -autorecon3
>> recon-all -autorecon2 -autorecon3
>> recon-all -make all
>>
>> Please advise, I could FTP one subject to you for suggestions. Again,
>> edits
>> here are all voxel deletions and not additions to wm.mgz.
>> Thank you,
>> Octavian
>>
>>
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[Freesurfer] wm edits not incorporated on recon-all rerun

[Octavian Lie]

Dear All,

I am stuck. Several brains I segment need both wm and pial edits, typically
deleting incorrectly incorporated voxels, such as dural voxels for pia, and
basal temporal hyperintensity artifact or bright dural voxels included due
to partial volume effects for wm.

I edited brainmask.mgz or brain.finalsurfs.manedit.mgz for pia, and wm.mgz
for wm. Rerunning recon-all led as expected to pial correction, however wm
edits did not end up in ?h.white, despite increasingly desperate efforts
and commands:

recon-all -autorecon2-wm -autorecon3
recon-all -autorecon2 -autorecon3
recon-all -make all

Please advise, I could FTP one subject to you for suggestions. Again, edits
here are all voxel deletions and not additions to wm.mgz.
Thank you,
Octavian
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Re: [Freesurfer] Recon-all after edits

[Octavian Lie]

Hello Bruce,

I think this ties to one of my previous questions. Most of the volumes I
processed need both wm and pial edits (typically deleting incorrectly added
voxels for both). More recently, I was editing wm.mgz for wm and
brainmask.mgz for pial. From the wiki, if changes are made for both wm/pia,
one can run recon-all -autorecon2 -autorecon3 and both changes would be
incorporated, however with some volumes this does not happen: pial edits
are incorporated correctly, but wm edits are not, I am not sure why, event
though FS6.0.0 sees edits (running recon-all with -showedits points to
edits in sm.mgz as well, and those edits propagate into filled.mgz. So
next, I plan editing brain.finalsurfs.manedit.mgz for pia ( it turns out
one cannot edit this also for wm when that means deleting voxels for wm),
wm.mgz for wm, then run -autorecon2-wm -autorecon3. Is this a strategy, and
if there are alternatives, please let me know. Also, for some reason,
running recon with '-make all'  does not seem to work.

Thank you,

Octavian


On Thu, Mar 30, 2017 at 8:51 AM, Bruce Fischl 
wrote:

> Hi Manuel
>
> -autorecon2-cp runs all the steps that autorecon2-wm does so it is
> redundant. If you run autorecon2-cp and autorecon3 you will get everything
> (unless you edit the aseg)
>
> cheers
> Bruce
> On Thu, 30 Mar 2017, Manuel Delgado wrote:
>
> > Dear list,
> > There is an issue that I have been concerned about since the beginning
> of my
> > FS learning, as I have found somehow contradictory information in the
> > tutorials. Is there a way to do an only recon-all after all the edits
> have
> > been made to a subject? For example, if you have edited all the possible
> > steps (skullstrip, control points, wm and pial surface) is it possible to
> > use all the flags for each step in one only step? Something like:
> > recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3
> -subjid
> > 
> >
> > Or on the other hand each step needs its own recon-all with its
> appropriate
> > flag?
> > Thank you
> >
> > --
> > Manuel Delgado Alvarado, MD
> > Neurology Department
> > Neuroimaging Unit
> > Valdecilla Biomedical Research Institute, IDIVAL
> > Santander, SPAIN
> >
> >
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[Freesurfer] Fwd: -dura_thresh

[Octavian Lie]

Can anybody comment on the new dura_thresh flag? See below,

Many thanks,

Octavian.

-- Forwarded message --
From: Octavian Lie 
Date: Sat, Mar 11, 2017 at 9:28 AM
Subject: -dura_thresh
To: "freesurfer@nmr.mgh.harvard.edu" 


Dear All,

In FS6.0.0, this flag is added to manually adjust watershed threshold
instead of its automatic calculation. I went back to the original paper by
Segonne et al, and I could identify the prefllooding height h and the post
watershed threshold t. I assume the flag refers to the latter.
Since the threshold varies between subjects, where is it specified in the
log file of a recon-all run?
Also, could you indicate a (narrow) range one could start with if trying to
manually adjust a run, based on your experience? Also, what is the
watershed direction based on t (higher t values lead to more aggressive
dura removal, or the other way around?

Thank you very much,

Octavian
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Re: [Freesurfer] WM/pial edits

[Octavian Lie]

Dear All,


Please advise. Some of the dural enclosure defects involve both wm and pia
surfaces (wm/pia extending to dura), so in those cases, correcting pia will
also touch the wm. Editing wm in wm.mgz and running recon-all
-autorecon2-wm -autorecon3 ameliorates but does not solve the wm defect
issue (some wm in some places still extending (albeit less) outside to
encompass some dural segments). At this point, to options I see are:
- to edit brainmask.mgz for pial surface, but because wm will be touched by
this correction, to run the whole -autorecon2 -autorecon 3
- to edit brain.finalsurfs.mgz for pial, then run -autorecon -pial, but I
do not know what this does to wm since wm is upstream.

Thank you,

Octavian









On Fri, Mar 10, 2017 at 9:51 AM, Bruce Fischl 
wrote:

> Hi Octavian
>
> if you want to regenerate the pial surface you have to run autorecon3 also.
>
> And I don't think you want to edit the wm.mgz for wm edits. Probably you
> should edit brain.finalsurfs.mgz for both wm and pial. Can someone who has
> done more recent recons than I have confirm this?
>
> cheers
> Bruce
>
>
>
> On Thu, 9 Mar 2017, Octavian Lie wrote:
>
> Dear All,
>>
>> A simple issue of precedence. In the recon-all pipeline, wm edits take
>> precedence to pial edits.
>> If there are both wm and pial defects, should one apply edits
>> sequentially,
>> say on brainmask.mgz (first wm edits, rerun recon-all say recon-all
>> -autorecon2 -wm, then do pial edits, rerun recon-all say recon-all
>> -autorecon2 -pial) or to some extent pial edits influence the final
>> surface
>> generation in conjunction to wm edits (understood that the latter may
>> influence more the final form than the former -pial- edits), in that case
>> one may do both edits, then run -autorecon2 -wm only.
>>
>> Please advise,
>> Octavian
>>
>>
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[Freesurfer] -dura_thresh

[Octavian Lie]

Dear All,

In FS6.0.0, this flag is added to manually adjust watershed threshold
instead of its automatic calculation. I went back to the original paper by
Segonne et al, and I could identify the prefllooding height h and the post
watershed threshold t. I assume the flag refers to the latter.
Since the threshold varies between subjects, where is it specified in the
log file of a recon-all run?
Also, could you indicate a (narrow) range one could start with if trying to
manually adjust a run, based on your experience? Also, what is the
watershed direction based on t (higher t values lead to more aggressive
dura removal, or the other way around?

Thank you very much,

Octavian
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[Freesurfer] WM/pial edits

[Octavian Lie]

Dear All,

A simple issue of precedence. In the recon-all pipeline, wm edits take
precedence to pial edits.
If there are both wm and pial defects, should one apply edits sequentially,
say on brainmask.mgz (first wm edits, rerun recon-all say recon-all
-autorecon2 -wm, then do pial edits, rerun recon-all say recon-all
-autorecon2 -pial) or to some extent pial edits influence the final surface
generation in conjunction to wm edits (understood that the latter may
influence more the final form than the former -pial- edits), in that case
one may do both edits, then run -autorecon2 -wm only.

Please advise,
Octavian
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[Freesurfer] -FLAIRpial; T2 SPACE

[Octavian Lie]

Dear All,

Our MPRAGE and T2 SPACE FLAIR sequences are acquired at times during two
different scans, and the MPRAGE seq further gets reoriented in a pipeline
upstream of the Freesurfer step.
For best results, does the FLAIR volume have to be reoriented (and
resliced) in a rigid registration to the MPRAGE before recon-all -all
stage, or it does not matter?

Thank you,

Octavian
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[Freesurfer] How to realign a surface in matlab to a realigned parent volume

[Octavian Lie]

Dear All,

I ran recon-all and generated a brain.mgz and say, lh.pial.
I converted brain.mgz to brain.nii, imported the latter to matlab/spm and
realigned it to rbrain.nii, generating a transform matrix
M=rbrain.reorient.mat.
if MM is the header for rbrain.nii, the header O for the original brain.nii
can be calculated with
O=inv(M) *MM.

How do I reorient the lh.pial to the rbrain.nii? I suppose I need a reader
for the pial header in matlab.

Many thanks,

Octavian
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Re: [Freesurfer] read_annotation error?

[Octavian Lie]

Dear Doug,

I figured it out.
I wanted to relate a set of points on the pial surface to their
corresponding Desikan indices and label names.
If


[vertices, label, colortable] = read_annotation([some-path
'\rh.aparc.annot'], 0);

x=unique(label);
y=sort(colortable.table(:,5));


Points labeled with 0 in x would correspond to index 1639705 in y
Label 3294840 in y does not correspond to any points on the surface, and
sends to corpus callosum.

Thank you,

Octavian



On Fri, Mar 6, 2015 at 10:18 AM, Douglas N Greve 
wrote:

>
> The 0 index is always "unknown". What problem does the other issue
> cause? It may be that there are just some items in the color table that
> are not represented in the annotation
> doug
>
> On 03/05/2015 09:05 PM, Octavian Lie wrote:
> > Dear Bruce,
> >
> > Reading the doc for read_annotation, it suggests that label entry
> > values should correspond to the colortable.table(:,5) indices. I
> > wanted to use it on Desikan annotation atlas and find annotation scout
> > names for selected cortical points:
> >
> >
> >
> > [vertices, label, colortable] = read_annotation([some-path
> > '\rh.aparc.annot'], 0);
> >
> > x=unique(label);
> > y=sort(colortable.table(:,5));
> >
> > it turns out that for any of several surfaces and their
> > corresponding rh and lh aparc.annot I tried, x is not equal to y.
> > Invariably,
> > x contains a label index 0 not present in y, and y contains indices
> > 1639705 and 3294840 not present in x. All the other label indices
> > match. I do not believe destrieux annot atlas has the same problem,
> > but I need to use desikan's.
> > Please confirm this general behavior and advise.
> > Thank you, as always,
> >
> > Octavian
> >
> >
> >
> >
> >
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> --
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> MGH-NMR Center
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Re: [Freesurfer] read_annotation error?

[Octavian Lie]

Dear Bruce,

Reading the doc for read_annotation, it suggests that label entry
values should correspond to the colortable.table(:,5) indices. I wanted to
use it on Desikan annotation atlas and find annotation scout names for
selected cortical points:



[vertices, label, colortable] = read_annotation([some-path
'\rh.aparc.annot'], 0);

x=unique(label);
y=sort(colortable.table(:,5));

it turns out that for any of several surfaces and their corresponding rh
and lh aparc.annot I tried, x is not equal to y. Invariably,
x contains a label index 0 not present in y, and y contains indices 1639705
and 3294840 not present in x. All the other label indices match. I do not
believe destrieux annot atlas has the same problem, but I need to use
desikan's.
Please confirm this general behavior and advise.
Thank you, as always,

Octavian
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Re: [Freesurfer] Fwd: Fwd: Eccentric lesions

[Octavian Lie]

I tried, here is the command:

mris_make_surfaces -cover_seg mri/aseg.mgz subjid lh

and the last 5 lines of the run:

...
smoothing surface for 5 iterations...
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
creating distance transform volume from segmentation
ERROR: mris_make_surfaces-MRIcheckVolDims: volume1 height=256 != volume2
height=1.


If this is it and not working, I wonder that editing the aseg to exclude
the nonlesional GM outside the pia, but leaving/ adding lesional GM of
interest, either under the GM label or a custom label would allow create a
'proper' volume, followed by surface generation. I known this is doable,
the question is whether the generated surface can be registered to sphere
and whether DK atlas can be applied (this is a more general question,
whether any surface generated outside the default recon-all pathway can be
registered to sphere and in effect become "pia" or another classical
boundary surface?)

example after labeling the lesion as 'o' (other):

% generate mask from aseg
cd /usr/local/fs5.3/freesurfer/subjects/subjid
mris_fill -c -r 0.1 surf/rh.pial mri/rh.pial.filled.mgz && \
mris_fill -c -r 0.1 surf/lh.pial mri/lh.pial.filled.mgz && \
mri_concat --combine --i mri/rh.pial.filled.mgz --i mri/lh.pial.filled.mgz
--o mri/pial.filled.mgz && \
cd ./mri && \
mri_binarize --i aseg.mgz --match o  --o lesion.mask.mgz && \
fscalc pial.filled.mgz add lesion.mask.mgz -o pialmask.mgz && \
mri_convert brain.mgz brain.float.mgz -odt float && \
mri_mask brain.float.mgz pialmask.mgz pialbrain.mgz

% generate new 'pial' surface:
mri_tessellate mri/pialbrain.mgz -a surf/lh.pialbrain.pial

Please advise,

Octavian
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Re: [Freesurfer] Fwd: Eccentric lesions

[Octavian Lie]

It looks like there is only gray matter (int 42), similar to cortical
ribbon gray, no white matter in that gyrus in aseg, both in the original
recon, and after painting gyral centers in brainmask.
Octavian

On Tue, Nov 25, 2014 at 7:51 AM, Octavian Lie 
wrote:

> Dear Bruce,
>
> I am not sure how an ok aseg.mgz would look like for a lesion like that,
> but it looks like it includes one larger gyrus excluded by the pia, see
> attached, I would be happy to retrieve that one as it is the bulkiest of
> all the ones left out.
> Thank you,
>
> Octavian
>
> On Tue, Nov 25, 2014 at 7:38 AM, Bruce Fischl 
> wrote:
>
>> Hi Octavian
>>
>> I wouldn't use control points since it really isn't healthy wm. The only
>> thing you can do is edit the wm.mgz and possibly also the brainmask, but
>> it's so abnormal looking you may not be able to get accurate surfaces.
>> How does the aseg look? If it is ok there may be one other option.
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 25 Nov 2014, Octavian Lie wrote:
>>
>> > Dear All,
>> > any suggestion about this type of problem? I tried control points
>> through
>> > the middle/axis of the atrophic gyri (intensity 30-90 in T1 or
>> brainmask),
>> > wm.mgz edits through the same (adding from brainmask by cloning those
>> > voxels; painting 110; or 255 brush), and modifying brainmask directly by
>> > painting 110 internsity voxels through the same (gyri interiors, where
>> wm is
>> > supposed to be). Did not work, the atrophic gyri continue to remain
>> outside
>> > the pia. Again, this is an example of an eccentric lesion with gyral
>> > atrophy, without interruption in the gray matter ribbon but very faint
>> wm
>> > signal through the base of the affected gyri.
>> > Thanks,
>> > Octavian
>> >
>> >
>> >
>> > -- Forwarded message --
>> > From: Octavian Lie 
>> > Date: Tue, Nov 18, 2014 at 10:50 AM
>> > Subject: Eccentric lesions
>> > To: "freesurfer@nmr.mgh.harvard.edu" 
>> >
>> >
>> > Dear All,
>> >
>> > I am interested at getting as good pial/cortical reconstructions as
>> possible
>> > on a series of epilepsy pt scans, some showing eccentric (cortical)
>> lesions
>> > (focal encephalomalacias, infarcts, or after focal resections). One
>> > particularly difficult lesion type to get an accurate cortical surface
>> is
>> > where there are prongs of grey matter bulging out (like a bag of worms),
>> > (mostly) without visible wm, see attached picture. These prongs are
>> > maintained in the brainmask.mgz and brain.finalsurfs.mgz, but not
>> included
>> > in the pia with the default recon. Lesion voxel intensities vary from
>> 30-90.
>> > I tried cp, wm edits (using brainmask or T1 as referece), both, did not
>> > matter, it did not work.
>> >
>> > Since I am not intested in wm/subcortical segmentation but just in a
>> good
>> > pia, I was wondering if I 'create' thin wm tracts through the center of
>> > these gm prongs to help pial segmentation. If this is a valid option,
>> should
>> > I create those in brainmask, brain.finalsurfs or wm.mgz, and should I
>> use
>> > 110 or 255 for the brush?
>> > Any other suggestions are appreciated. Nevertheless, I know there is a
>> lot
>> > of tweaking of each lesion, and I try for more of a global approach to
>> these
>> > kinds of lesions.
>> >
>> > Thank you,
>> >
>> > Octavian.
>> >
>> >
>> >
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[Freesurfer] pial mask

[Octavian Lie]

Dear all,

After running the recon-all on a subject, I needed to create a 'pial'
surface to include the hippocampi, which are not included well in the pial
reconstruction. So I generated a mask and used it to mask brain.mgz.

1. All well, except that in both the mask and the masked brain volume
(readybrain.mgz, see below), the fill extends with a variable layer of
about 1 voxel) above the pial red contour in some areas (see the top,
leading me to believe that the red contours we use when editing are not the
actual pial surfaces, but some interpolations of the actual calculated pial
surface. If this is true, then there may be some editing errors when using
these contours. Another explanation could be the resolution of the
mris_fill.
Please let me know which is the case, and how to fix it so that the mask
closely follows the red contour.

2. I need to generate a surface from readybrain.mgz, preferably that can be
registered to the sphere.reg and on which cortical parcellation (DK atlass)
can be applied. Is there a way? If not, I would still like to know how to
generate the surface of this volume.

Thank you,

Octavian

Here is the code I used:

cd /usr/local/fs5.3/freesurfer/subjects/subjid

mris_fill -c -r 0.1 surf/rh.pial mri/rh.pial.filled.mgz && \
mris_fill -c -r 0.1 surf/lh.pial mri/lh.pial.filled.mgz && \
mri_concat --combine --i mri/rh.pial.filled.mgz --i mri/lh.pial.filled.mgz
--o mri/pial.filled.mgz && \
cd ./mri && \
mri_binarize --i aseg.mgz --match 5 --match 9 --match 10 --match 14 --match
17 --match 18 --match 19\
 --match 25 --match 31 --match 44 --match 48 --match 49 --match 53 --match
54 --match 55 --match 57\
 --match 63 --match 86 --match 96 --match 97 --match 105 --match 106
--match 114 --match 115\
 --match 195 --match 199 --match 203 --match 204 --match 205 --match 216
--match 222 --match 225\
 --match 507 --match 557 --match 1200 --match 1201 --match 1205 --match
1206 --match 2200 --match 2201\
 --match 2205 --match 2206 --o hippoamy.mask.mgz && \
fscalc pial.filled.mgz add hippoamy.mask.mgz -o epimask.mgz && \
mri_convert brain.mgz brain.float.mgz -odt float && \
mri_mask brain.float.mgz epimask.mgz readybrain.mgz
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[Freesurfer] Fwd: outer pial error

[Octavian Lie]

Solved it, thank you



-- Forwarded message --
From: Octavian Lie 
Date: Mon, Nov 17, 2014 at 8:11 AM
Subject: outer pial error
To: "freesurfer@nmr.mgh.harvard.edu" 


Dear All,
I tried to get an outer pial surface on a previously processed pt subjid,
and I got the following error.
(recon-all was running another subject in a separate window, for what's
worth)
Please advise,

Octavian


recon-all -localGI -s subjid

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
INFO: SUBJECTS_DIR is /usr/local/fs5.3/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/fs5.3/freesurfer
-rw-rw-r-- 1 ovl ovl 3224039 Nov 17 07:58
/usr/local/fs5.3/freesurfer/subjects/subjid/scripts/recon-all.log
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/fs5.3/freesurfer/subjects/subjid/surf
#
#@# Local Gyrification Index lh Mon Nov 17 08:03:50 CST 2014

 mris_compute_lgi --i lh.pial

=
rm -Rf
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
*make_outer_surface('/usr/local/fs5.3/freesurfer/subjects/*
*subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/fs5.3/freesurfer/subjects/**subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit*
=
ERROR:: Too many arguments.
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s subjid exited with ERRORS at Mon Nov 17 08:03:54 CST 2014
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[Freesurfer] Fwd: outer pial error

[Octavian Lie]

It could be that the error is due to a matlab path issue according to some
previous posts, and it is true I cannot find matlab with getmatlab command.
I have trouble setting up MATLABPATH.

First, I can open matlab from terminal with commands matlab12 or matlab 13,
I have 2 versions that I use for other applications, located at
 /usr/local/MATLAB/R2012b and  /usr/local/MATLAB/R2013a (the files matlab12
and matlab13 used to call matlab are in /usr/local/bin)
and I have a startup.m file in $HOME/matlab where the freesurfer matlab
files are visible to matlab.

However, when I call env from terminal, matlabpath does not show up.

I must mention that the default shell was bash, and I changed it to
.tcsh when installing FS, which works well, without issues


I guess I have to modify my /etc/csh.cshrc file to include matlab path, but
several trials have failed, example

setenv MATLABPATH /usr/local/MATLAB/R2012b does not help when calling getmatlab

Please advise,

Thank you,

Octavian










-- Forwarded message --
From: Octavian Lie 
Date: Mon, Nov 17, 2014 at 8:11 AM
Subject: outer pial error
To: "freesurfer@nmr.mgh.harvard.edu" 


Dear All,
I tried to get an outer pial surface on a previously processed pt subjid,
and I got the following error.
(recon-all was running another subject in a separate window, for what's
worth)
Please advise,

Octavian


recon-all -localGI -s subjid

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
INFO: SUBJECTS_DIR is /usr/local/fs5.3/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/fs5.3/freesurfer
-rw-rw-r-- 1 ovl ovl 3224039 Nov 17 07:58
/usr/local/fs5.3/freesurfer/subjects/subjid/scripts/recon-all.log
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/fs5.3/freesurfer/subjects/subjid/surf
#
#@# Local Gyrification Index lh Mon Nov 17 08:03:50 CST 2014

 mris_compute_lgi --i lh.pial

=
rm -Rf
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
*make_outer_surface('/usr/local/fs5.3/freesurfer/subjects/*
*subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/fs5.3/freesurfer/subjects/**subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit*
=
ERROR:: Too many arguments.
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s subjid exited with ERRORS at Mon Nov 17 08:03:54 CST 2014
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[Freesurfer] outer pial error

[Octavian Lie]

Dear All,
I tried to get an outer pial surface on a previously processed pt subjid,
and I got the following error.
(recon-all was running another subject in a separate window, for what's
worth)
Please advise,

Octavian


recon-all -localGI -s subjid

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
INFO: SUBJECTS_DIR is /usr/local/fs5.3/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/fs5.3/freesurfer
-rw-rw-r-- 1 ovl ovl 3224039 Nov 17 07:58
/usr/local/fs5.3/freesurfer/subjects/subjid/scripts/recon-all.log
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/fs5.3/freesurfer/subjects/subjid/surf
#
#@# Local Gyrification Index lh Mon Nov 17 08:03:50 CST 2014

 mris_compute_lgi --i lh.pial

=
rm -Rf
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
*make_outer_surface('/usr/local/fs5.3/freesurfer/subjects/*
*subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/fs5.3/freesurfer/subjects/**subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit*
=
ERROR:: Too many arguments.
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s subjid exited with ERRORS at Mon Nov 17 08:03:54 CST 2014
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[Freesurfer] Cortex/volume parcellation

[Octavian Lie]

Dear all,

Is there a way to generate random or seed-based whole cortical (surface) or
brain (volumetric) parcellations in freesurfer or plugins, generating n
equal area (volume) scouts, where the user can select the n?
Thank you,

Octavian
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Re: [Freesurfer] edit failure

[Octavian Lie]

Dear Bruce,

It worked, I transferred it and is ready for view.
The original recon was with the command
recon-all -3T -openmp 8 -notal-check (the raw volume was analyze).
I noted a small gyrus excluded from the surfaces, located in the right
hemisphere posteriorly; the recon also did not include two other regions in
the left hemisphere (one mesial gyrus, and a wedge-shaped region, also
posteriorly located), but I am insterested mainly in the right hemisphere,
and I suspect the solution would be the same.
After the original recon, I did some pial editing (although not perfect),
and tried control points and wm/topological defect corrections. As suchs,
the wm.mgz included was edited to extend into the excluded areas for
correction.
Thank you for helping, as always. Please let me know if there is a fix,
such as cloning voxels from T1.mgz into brain.finalsufs,manedit.mgz.

Octavian

On Mon, Nov 10, 2014 at 11:09 AM, Bruce Fischl 
wrote:

> try changing the local dir to /usr/local/fs5.3/freesurfer/subjects and just
> putting the file without a path
>
> cheers
> Bruce
>
>
> On Mon, 10 Nov 2014, Octavian Lie wrote:
>
> > Thank you, Bruce
> >
> > I tried to upload the subject (tar.gz, 183 Mb) to the ftp, followed
> > instructions
> >
> > ftp surfer.nmr.mgh.harvard.edu
> > anonymous
> > my email
> > cd transfer/incoming
> > put /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
> >
> > and I get this:
> >
> > local: /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
> remote:
> > /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
> > 200 PORT command successful. Consider using PASV.
> > 553 Could not create file.
> >
> > Please advise,
> >
> > Octavian
> >
> > On Sun, Nov 9, 2014 at 9:44 PM, Bruce Fischl  >
> > wrote:
> >   Hi Octavian
> >   If you upload the subject we will take a look
> >   Cheers
> >   Bruce
> >
> >
> >
> >   > On Nov 9, 2014, at 10:40 PM, Octavian Lie
> >wrote:
> >   >
> >   > Dear all,
> >   >
> >   > 1. in the attached there is a gyrus that does not incorporated
> >   into surfaces, whatever I do (wm edits/topological
> >   defects-cloning voxels from brainmask.mgz or T1.mgz into wm.mgz,
> >   save volume then run recon-all autorecon2-wm autorecon 3), or
> >   control points addition to wm in brainmask.mgz, then run the -cp
> >   flag. Is there any other solution left to clone the white matter
> >   (and pial voxels) left out? is brain.finalsurfs.manedit.mgz a
> >   solution?
> >   >
> >   > 2. Unrelated, after manual pial edits and reruning the
> >   recon-all autorecon-pial command, the pial surface generated is
> >   mostly OK, however where there have been heavy dura editing the
> >   surface looks granular. Is there a workaround (along with better
> >   hands), such as smoothing the final pia a bit more (preferably
> >   in the recon-all pipeline as to be convergent with other
> >   segmentation results).
> >   >
> >   > I appreciate your help,
> >   >
> >   > Octavian
> > > 
> > > 
> > > ___
> > > Freesurfer mailing list
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> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
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> >
> >
> > The information in this e-mail is intended only for the person to whom
> > it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
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> >
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Re: [Freesurfer] edit failure

[Octavian Lie]

Thank you, Bruce

I tried to upload the subject (tar.gz, 183 Mb) to the ftp, followed
instructions

ftp surfer.nmr.mgh.harvard.edu
anonymous
my email
cd transfer/incoming
put /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz

and I get this:

local: /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
remote: /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
200 PORT command successful. Consider using PASV.
553 Could not create file.

Please advise,

Octavian

On Sun, Nov 9, 2014 at 9:44 PM, Bruce Fischl 
wrote:

> Hi Octavian
> If you upload the subject we will take a look
> Cheers
> Bruce
>
>
>
> > On Nov 9, 2014, at 10:40 PM, Octavian Lie 
> wrote:
> >
> > Dear all,
> >
> > 1. in the attached there is a gyrus that does not incorporated into
> surfaces, whatever I do (wm edits/topological defects-cloning voxels from
> brainmask.mgz or T1.mgz into wm.mgz, save volume then run recon-all
> autorecon2-wm autorecon 3), or control points addition to wm in
> brainmask.mgz, then run the -cp flag. Is there any other solution left to
> clone the white matter (and pial voxels) left out? is
> brain.finalsurfs.manedit.mgz a solution?
> >
> > 2. Unrelated, after manual pial edits and reruning the recon-all
> autorecon-pial command, the pial surface generated is mostly OK, however
> where there have been heavy dura editing the surface looks granular. Is
> there a workaround (along with better hands), such as smoothing the final
> pia a bit more (preferably in the recon-all pipeline as to be convergent
> with other segmentation results).
> >
> > I appreciate your help,
> >
> > Octavian
> > 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>
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> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] Pial edits and wm control points.

[Octavian Lie]

Thank you, Bruce.

For point 1, a nice alternative would be to be able to edit brainmask.mgz
while T1.mgz is displayed instead.
As for the control points, I generated one set in freeview, but when saving
it with 'save as', it did not give me an option where to save it, and it
did it in 'home' and not in subjid/tmp, so recon-all did not take it, I
will try copy past that into  the /tmp folder and retry. Is this a set path
problem, and if so how can it be fixed.

thanks,

Octavian

On Sat, Nov 8, 2014 at 8:04 AM, Bruce Fischl 
wrote:

> I'll leave 1 for Ruopeng. For 2, usuually I'll do a little cluster ofr 3-4
> together in an area, then a big space to the next cluster, but probably
> even only 1 would be fine. 2-5mm is much denser than the cluster spacing
> needs to be. For 3, yes that is fine
>
>
> On Fri, 7 Nov 2014, Octavian Lie wrote:
>
>  Dear all,
>>
>> I am editing recon-all segmentation results in freeview using the recon
>> edit
>> function.
>> 1. Is there a way to complement the toggle between the brainmask.mgz and
>> T1.mgz, especially at the end of pial editing, before resubmitting the
>> saved
>> brainmask volume to recon-all? It would be nice to be able to see the
>> edited
>> voxels (the final ones remaining edited, after successive
>> deletions/clones) as a mask over the T1.mgz in freeview as the final check
>> before sending brainmask back to segmentation.
>>
>> 2. As far as control points go, the FS tutorial mentions that there is a
>> certain trial and error as to the no or density of control points to be
>> used. Still, the example fig in the tutorial shows control points spaced
>> about 2-5-voxels. Is this a good starting point in general?
>>
>> 3. Some of the segmentations need bit corrections in wm edits
>> (filling holes), missing wm in brainmask (control points with T1.mgz as
>> reference), and pial edits. It is OK if  all of these corrections are done
>> in a single step on brainmask.mgz with aux T1.mgz, then do
>> recon-all -autorecon2-cp -autorecon3 -subjid?
>>
>> Thank you for your tips,
>>
>> Octavian
>>
>>
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[Freesurfer] Pial edits and wm control points.

[Octavian Lie]

Dear all,

I am editing recon-all segmentation results in freeview using the recon
edit function.
1. Is there a way to complement the toggle between the brainmask.mgz and
T1.mgz, especially at the end of pial editing, before resubmitting the
saved brainmask volume to recon-all? It would be nice to be able to see the
edited voxels (the final ones remaining edited, after successive
deletions/clones) as a mask over the T1.mgz in freeview as the final check
before sending brainmask back to segmentation.

2. As far as control points go, the FS tutorial mentions that there is a
certain trial and error as to the no or density of control points to be
used. Still, the example fig in the tutorial shows control points spaced
about 2-5-voxels. Is this a good starting point in general?

3. Some of the segmentations need bit corrections in wm edits
(filling holes), missing wm in brainmask (control points with T1.mgz as
reference), and pial edits. It is OK if  all of these corrections are done
in a single step on brainmask.mgz with aux T1.mgz, then do
recon-all -autorecon2-cp -autorecon3 -subjid?

Thank you for your tips,

Octavian
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Re: [Freesurfer] notal-check/pial edits

[Octavian Lie]

I subscribe to the question above. Also, is there a flag that would make
recon throw a warning about tailarach registration issue, but not stop the
routine?
Thank you,

Octavian


On Thu, Nov 6, 2014 at 7:30 AM, John Epiktitos  wrote:

> Hi Bruce,
> if i have analyse format which is the right orientation to enter the data
> in freesurfer. Radiologically (r/l) or vise versa?
> John
>
> On Thu, Nov 6, 2014 at 3:21 PM, Bruce Fischl 
> wrote:
>
>> Hi Octavian
>>
>> does your data show in the proper orientation in freeview/tkmedit?
>> Analyze is a dangerous format as it doesn't contain direction cosine info
>> and hence even if it looks right you may have left/right swapped and not
>> know it.
>>
>> I don't think the spherical stuff needs tal, so if it runs through
>> without it you are fine.
>>
>> cheers
>> Bruce
>>
>> On Wed, 5 Nov 2014, Octavian Lie wrote:
>>
>>  Dear All,
>>>
>>> this is very basic. I have Analyze volumes, and I was suggested to use
>>> -notal-check to bypass the 3rd recon step. I wanted to make sure skipping
>>> the T registration step would not have the potential to mess up the
>>> spherical registration in autorecon3 in any way on a case by case basis.
>>> I
>>> do not want to spend time in tkregister2 unless is necessary for the
>>> spherical registration step.
>>>
>>> Also, I anticipate losts of pial edits (let's exclude the wm edits/cp),
>>> and
>>> I wanted to make sure different command scenarios are correct:
>>>
>>> 1. recon-all -autorecon1 -subjid
>>> edit pia, save brainmask.mgz
>>> recon-all -autorecon2 -autorecon3 -subjid
>>>
>>> 2. recon-all -autorecon1 -autorecon2 -subjid
>>> edit pia, save brainmask.mgz
>>> recon-all -autorecon2-pial -autorecon3 -subjid
>>> (preferred)
>>>
>>> 3. recon-all -subjid
>>> edit pia, save brainmask.mgz
>>> recon-all -autorecon-pial -subjid
>>>
>>> Please comment,
>>> thank you,
>>> Octavian
>>>
>>>
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[Freesurfer] notal-check/pial edits

[Octavian Lie]

Dear All,

this is very basic. I have Analyze volumes, and I was suggested to use
-notal-check to bypass the 3rd recon step. I wanted to make sure skipping
the T registration step would not have the potential to mess up the
spherical registration in autorecon3 in any way on a case by case basis. I
do not want to spend time in tkregister2 unless is necessary for the
spherical registration step.

Also, I anticipate losts of pial edits (let's exclude the wm edits/cp), and
I wanted to make sure different command scenarios are correct:

1. recon-all -autorecon1 -subjid
edit pia, save brainmask.mgz
recon-all -autorecon2 -autorecon3 -subjid

2. recon-all -autorecon1 -autorecon2 -subjid
edit pia, save brainmask.mgz
recon-all -autorecon2-pial -autorecon3 -subjid
(preferred)

3. recon-all -subjid
edit pia, save brainmask.mgz
recon-all -autorecon-pial -subjid

Please comment,
thank you,
Octavian
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[Freesurfer] surface reorientation in sinc with volume

[Octavian Lie]

Dear All

I reoriented a volume on exporting to analyze format for an application


mri_convert -i path to file/T1.mgz --out_orientation PSR -o path to
file/T1reoriented.mgz
mri_convert -ot analyze -i path to file/T1reoriented.mgz -o path to
file/T1reorientedPSR.img

I need to reorient from the command line the original pial surfaces
(?h.pial) generated from the recon-all process to new surfaces to
match the new T1 orientation (T1 reorientedPSR).

Thank you, please advise,

Octavian
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Re: [Freesurfer] pial erosion/downsampling

[Octavian Lie]

 Thank you,

I want to merge the pial eroded (of white expanded) and downsampled
surfaces of the two hemispheres in a new surface (generate a new,
continuous,  surface/mesh, no holes, no self intersections). The
question is
whether pial freesurfer atlases and spherical registration would be
applicable to this surface too,
Octavian

On Wed, Jan 8, 2014 at 11:54 AM, Bruce Fischl
 wrote:
> can you cc the list? I don't know what you mean by "merge"
>
> On Wed, 8 Jan 2014, Octavian Lie wrote:
>
>> Thank you,
>>
>> I want to merge the pial eroded (of white expanded) and downsampled
>> surfaces of the two hemispheres in a new surface. The question is
>> whether pial freesurfer atlases and spherical registration would be
>> applicable to this surface too,
>> Octavian
>>
>>
>>
>
>
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[Freesurfer] pial erosion/downsampling

[Octavian Lie]

 Dear All,

1. I need to erode the ?h.pial surfaces be exactly 3 mm, then
2. I need to downsample each of the eroded surfaces to 7500 vertices each, then
(3. Merge the downsampled surfaces (whether or not an intermediary
voxelizing step is involved))

I would appreciate any help with command syntax.
If this is possible, is there a way to warp/ preserve the relationship
of the output with aparc.anot labels and surface based registration
/sphere.reg in freesurfer?
Trying this route to a 4-layer BEM...

Thank you,

Octavian
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Re: [Freesurfer] Motion correction for SPACE FLAIR

[Octavian Lie]

Dear Bruce,

Best wishes for 2014!

I will heed your advice and cc to the list. Indeed, the MGH protocol I
obtained from Andre has one acquisition (NSA).
Related, I cc this post:

We have been trying adaptations of the T2spaceFLAIR MGH protocol on
our Phillips 3T scanners (sequences called VISTA). Incorporation of
the T2 space FLAIR has been mostly successful at editing out the dura
from the pial surface. The only concern are minute differences
occasionally appearing as small indentations (at most times <1-2mm)
between the woFLAIR.pial and the final pial surfaces, including in
intrasulcal (duraless) areas; the amount of these small mismatches is
variable from patient to patients, with some trials with almost
perfect overlap, and others with visible, if small, differences. I
wonder if this has been your experience too, and if this is due mostly
to bb registration limits or to differences in pixel bandwidth between
mprage and space flair sequences (in our case, see below).
In FSwiki, the recommendation is that T2 space flair “should be
bandwidth, geometry and readout matched to the mprage”.

1. Speaking about pixel bandwidth, logistics most likely would not
allow application of a MEMPR sequence on our Phillips. According to
Siemens MPRAGE MGH specs, "exceptions indicate that if a multiple echo
sequence is not available, one should choose a bandwidth of 195
Hz/pixel for the MPRAGE". In that case/ using the Siemens Trio MPRAGE
protocol as if the MEMPR is not available, how one would adjust the
bandwidth in T2spaceFLAIR protocol (currently ~650 in the Siemens
space flair and MEMPR protocols)  to "match" it to the "simple" MPRAGE
protocol (decreasing it to 195 ?). Would it be a workaround? (Please
comment on the Siemens case, obviously, I do not expect any light on
Phillips without further testing).
2. Could you clarify what geometry matched means?
Please advise,

Thank you,

Octavian

On Fri, Jan 3, 2014 at 9:12 PM, Bruce Fischl  wrote:
> Hi Octavian
>
> can you cc the list so that others can answer? What is NSA? We don't have a
> ton of experience with it, but 1 has seemed ok (not sure if we've ever tried
> two)
> Bruce
>
>
>
> On Thu, 2 Jan 2014, Octavian Lie wrote:
>
>> Dear Bruce,
>>
>> Thank you. We used one vs 2 NSA T2 space FLAIR sequences, without a
>> consistent difference in results, with the 2-NSA run obviously doubling
>> the
>> scan time. Is there a preferred number of NSA you recommend, or we should
>> be
>> fine with one? Both are at resolution 1X1X1 mm.
>> Thank you,
>>
>> Octavian
>>
>>
>>
>> On Thu, Jan 2, 2014 at 11:56 AM, Bruce Fischl 
>> wrote:
>>   Hi Octaviaan
>>   no, not really. You should motion correct and average them using
>>   something like mri_motion_correct*
>>
>>   We do typically bandwidth/readout match them to the memprages so
>>   that there is no differential distortion
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Wed, 1 Jan 2014, Octavian Lie wrote:
>>
>> Dear All,
>>
>> We recently implemented pial correction using T2
>> space FLAIR with freesurfer
>> v 5.3, mostly successfully. We use 2-3 MPRAGE
>> (sagittal + axial and/or
>> coronal) volumes as 001.mgz, 002/003.mgz for the
>> motion correction step in
>> recon-all pipeline.
>> The typical times for acquiring space FLAIR in our
>> settings vary from 2.5 to
>> 6 min, depending on the resolution/NSA no. I was
>> wondering how freesurfer
>> deals with motion artifacts in the space FLAIR
>> sequence (especially with
>> longer acquisition times), and if there is a
>> strategy to minimize motion
>> distortion with these (such as getting second runs
>> for averaging, etc).
>> Please advise,
>>
>> Octavian.
>>
>>
>>
>>
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>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
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>> and properly
>> dispose of the e-mail.
>>
>>
>>
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[Freesurfer] Motion correction for SPACE FLAIR

[Octavian Lie]

Dear All,

We recently implemented pial correction using T2 space FLAIR with
freesurfer v 5.3, mostly successfully. We use 2-3 MPRAGE (sagittal + axial
and/or coronal) volumes as 001.mgz, 002/003.mgz for the motion correction
step in recon-all pipeline.
The typical times for acquiring space FLAIR in our settings vary from 2.5
to 6 min, depending on the resolution/NSA no. I was wondering how
freesurfer deals with motion artifacts in the space FLAIR sequence
(especially with longer acquisition times), and if there is a strategy to
minimize motion distortion with these (such as getting second runs for
averaging, etc).
Please advise,

Octavian.
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[Freesurfer] fsl & T2pial

[Octavian Lie]

Dear All,

I plan starting running the -FLAIRpial flag for pial refinement, after
recently upgrading freesurfer to dev (12/19/2013), centos6 86X64 build. I
installed the new fs according to the wiki guidelines.
I read on the forum that FSL_DIR has to be set up, and FSL has to be
installed for bbregister to work. The default wiki installation does not
set FSL_DIR.

I found a bbregister file dated 12/17/2013 by Doug in freesurfer/bin, so it
could be that the above issue has been solved, please confirm.

Octavian
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Re: [Freesurfer] Freesurfer installation error

[Octavian Lie]

solved, thank you,
Octavian


On Sat, Dec 21, 2013 at 11:55 AM, Octavian Lie wrote:

> Dear All,
>
> I downloaded/installed freesurfer-Linux-centos6_x86_64-dev version
> (12/19/2013) on my ubuntu 12.04 using tcsh, also fixed missing libnetcdf
> libraries missing in my distro, here is fs home directory:
>
> FREESURFER_HOME   /usr/local/fs5.3/freesurfer
> FSFAST_HOME   /usr/local/fs5.3/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/fs5.3/freesurfer/subjects
> MNI_DIR   /usr/local/fs5.3/freesurfer/mni
>
> Testing using the commands on the testing page went OK, however, if I
> close the terminal, open another one, commands are not recognized, and I
> have to reset freesurfer home every time I open a terminal with
>
> setenv FREESURFER_HOME /freesurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
> I thought this is a sudo issue, however if I use
>
> sudo setenv FREESURFER_HOME /usr/local/fs5.3/freesurfer, it tells me:
>
> sudo: setenv: command not found
>
>
> I mention I changed the default shell from bash to tcsh recently,
> Please advise,
>
> Octavian
>
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Re: [Freesurfer] Freesurfer dev install/ testing error

[Octavian Lie]

solved, thank you,
Octavian


On Fri, Dec 20, 2013 at 2:44 PM, Octavian Lie wrote:

> Dear All,
>
> I have ubuntu 12.4, and downloaded/installed the dev (12/19/2013) version
> of Freesurfer (I used previously version 5.1). Installation was uneventful,
> including getting the return to command
>
> > source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
> FREESURFER_HOME   /usr/local/fs5.3/freesurfer
> FSFAST_HOME   /usr/local/fs5.3/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/fs5.3/freesurfer/subjects
> MNI_DIR   /usr/local/fs5.3/freesurfer/mni
>
> When testing Freesurfer with freeview or tkmedit bert commands, I get
> invariably the following error
>
> 'error while loading shared libraries: libnetcdf.so.6: cannot open shared
> object file: No such file or directory'
>
> Can you advise what I should do, including syntax (Gari has a similar
> problem, and he solved it "after reinstalling netCDF and updating the links
> (and some 64 bit packages missing too)").
>
> Please let me know what else I should add/ modify after
>
> sudo apt-get install libnetcdf6
>
> and what other packages and links have to be installed/ fixed
>
> Many thanks,
>
> Octavian
>
>
>
>
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[Freesurfer] jpeg compressed dicom mri convert error

[Octavian Lie]

Dear all,

I tried to run a subject's T1 starting with the dicom convert step (until
now, I used .nii volumes as imput, after dicom conversion in spm; I would
like to be able to use the dicom convert in freesurfer, since I have a
-T2pial step to refine pias afterwards, and it's easier this way).

I get the following mri_convert error about jpeg compression (this is the
only dicom output processed at our facility):

recon-all -s subj -i /home/ovl/Desktop/freesurferdicom/subj/T1/51129

Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
INFO: SUBJECTS_DIR is /usr/local/fs5.3/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/fs5.3/freesurfer
Linux Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/fs5.3/freesurfer/subjects/subj

mri_convert /home/ovl/Desktop/freesurferdicom/subj/T1/51129
/usr/local/fs5.3/freesurfer/subjects/subj/mri/orig/001.mgz

mri_convert /home/ovl/Desktop/freesurferdicom/subj/T1/51129
/usr/local/fs5.3/freesurfer/subjects/subj/mri/orig/001.mgz
$Id: mri_convert.c,v 1.206 2013/11/12 03:15:51 greve Exp $
reading from /home/ovl/Desktop/freesurferdicom/subj/T1/51129...
Starting DICOMRead2()
dcmfile = /home/ovl/Desktop/freesurferdicom/subj/T1/51129
dcmdir = /home/ovl/Desktop/freesurferdicom/subj/T1
Ref Series No = 302
Found 167 files, checking for dicoms
Found 165 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.999557 0.0285859 -0.00787544
Vs: -0.99956 0.028586 -0.00787546
Second Sorting
Counting frames
nframes = 1
nslices = 165
ndcmfiles = 165
PE Dir = ROW (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.4.70--
ERROR: the pixel data cannot be loaded as it is JPEG compressed.
   (Transfer Syntax UID: 1.2.840.10008.1.2.4.70)
jpegUID:   --1.2.840.10008.1.2.4--
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s subj exited with ERRORS at Sun Dec 22 21:22:11 CST 2013

For more details, see the log file
/usr/local/fs5.3/freesurfer/subjects/subj/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Is there a workaround in freesurfer?

Thank you,

Octavian
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[Freesurfer] Freesurfer installation testing tksurfer error

[Octavian Lie]

Dear All,

I have recently upgraded freesurfer (dev version 12/19/2013 centos6,
86X64) on my ubuntu 12.04 box, I previously used v 5.1(centos 4).

I fixed all other issues that I posted about (libnetcdf
missing,.tcshrc editing), now all seems to go well, including testing,
except

when I load tksurfer bert rh pial, I see it well, and I can use
tksurfer tools well, as expected; however, if I want to close the
window
displaying surfaces (either before or after closing tksurfer tools
gui), I cannot; the only way to kill the process and exit tksurfer is
to close the terminal. Also, if I try to maximize the same window, I
get the following error:


surfer: Error sending tcl command MoveToolWindow 65 656:
can't invoke "wm" command:  application has been destroyed
surfer: Error sending tcl command MoveToolWindow 65 1080:
can't invoke "wm" command:  application has been destroyed
surfer: Error sending tcl command MoveToolWindow 65 1080:
can't invoke "wm" command:  application has been destroyed
surfer: Error sending tcl command MoveToolWindow 65 1080:
can't invoke "wm" command:  application has been destroyed
surfer: Error sending tcl command MoveToolWindow 65 1080:
can't invoke "wm" command:  application has been destroyed

I loaded other subjects previously processed with v5.1 version, and I
have the same issue. All other guis, including tkmedit, freeview and
qdec work well.

Please advise,

Octavian
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[Freesurfer] Freesurfer installation error

[Octavian Lie]

Dear All,

I downloaded/installed freesurfer-Linux-centos6_x86_64-dev version
(12/19/2013) on my ubuntu 12.04 using tcsh, also fixed missing libnetcdf
libraries missing in my distro, here is fs home directory:

FREESURFER_HOME   /usr/local/fs5.3/freesurfer
FSFAST_HOME   /usr/local/fs5.3/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/fs5.3/freesurfer/subjects
MNI_DIR   /usr/local/fs5.3/freesurfer/mni

Testing using the commands on the testing page went OK, however, if I close
the terminal, open another one, commands are not recognized, and I have to
reset freesurfer home every time I open a terminal with

setenv FREESURFER_HOME /freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

I thought this is a sudo issue, however if I use

sudo setenv FREESURFER_HOME /usr/local/fs5.3/freesurfer, it tells me:

sudo: setenv: command not found


I mention I changed the default shell from bash to tcsh recently,
Please advise,

Octavian
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Re: [Freesurfer] Freesurfer dev install/ testing error

[Octavian Lie]

I forgot to mention that I downloaded the
freesurfer-Linux-centos6_x86_64-dev version (again 12/19/2013), and that
other lib files, such as libjpeg.so files (related to install issues on
some ubuntu systems according to the release notes) are stored in
/usr/lib/x86_64-linux-gnu/
 on my computer

Thank you,

Octavian


On Fri, Dec 20, 2013 at 2:44 PM, Octavian Lie wrote:

> Dear All,
>
> I have ubuntu 12.4, and downloaded/installed the dev (12/19/2013) version
> of Freesurfer (I used previously version 5.1). Installation was uneventful,
> including getting the return to command
>
> > source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
> FREESURFER_HOME   /usr/local/fs5.3/freesurfer
> FSFAST_HOME   /usr/local/fs5.3/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /usr/local/fs5.3/freesurfer/subjects
> MNI_DIR   /usr/local/fs5.3/freesurfer/mni
>
> When testing Freesurfer with freeview or tkmedit bert commands, I get
> invariably the following error
>
> 'error while loading shared libraries: libnetcdf.so.6: cannot open shared
> object file: No such file or directory'
>
> Can you advise what I should do, including syntax (Gari has a similar
> problem, and he solved it "after reinstalling netCDF and updating the links
> (and some 64 bit packages missing too)").
>
> Please let me know what else I should add/ modify after
>
> sudo apt-get install libnetcdf6
>
> and what other packages and links have to be installed/ fixed
>
> Many thanks,
>
> Octavian
>
>
>
>
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[Freesurfer] Freesurfer dev install/ testing error

[Octavian Lie]

Dear All,

I have ubuntu 12.4, and downloaded/installed the dev (12/19/2013) version
of Freesurfer (I used previously version 5.1). Installation was uneventful,
including getting the return to command

> source $FREESURFER_HOME/SetUpFreeSurfer.csh

FREESURFER_HOME   /usr/local/fs5.3/freesurfer
FSFAST_HOME   /usr/local/fs5.3/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/fs5.3/freesurfer/subjects
MNI_DIR   /usr/local/fs5.3/freesurfer/mni

When testing Freesurfer with freeview or tkmedit bert commands, I get
invariably the following error

'error while loading shared libraries: libnetcdf.so.6: cannot open shared
object file: No such file or directory'

Can you advise what I should do, including syntax (Gari has a similar
problem, and he solved it "after reinstalling netCDF and updating the links
(and some 64 bit packages missing too)").

Please let me know what else I should add/ modify after

sudo apt-get install libnetcdf6

and what other packages and links have to be installed/ fixed

Many thanks,

Octavian
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[Freesurfer] Export T1 volume and a set of points in the same space

[Octavian Lie]

Dear All,

I need to export a T1.mgz and  N points (Nx3 coordinates .mat file) of the
same volume in SPM12b. N are actually intracranial electrodes.
For this, I save T1.mgz as .nii prior to import into SPM.
Should I use volume index, volume RAS or surface RAS coordinates for N?
What other transforms I should apply to the .mat coordinate file so that
when read in SPM is in the same space as T1.nii?
Please advise,
Thank you,

Octavian.
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[Freesurfer] freesurfer upgrade

[Octavian Lie]

Dear All,

We use freesurfer in an automatic routine mainly for brain extraction/
parcellation schemes. I want to upgrade from 5.2 to 5.3 on a linux (ubuntu,
64bit) computer, but without surprises.
So:

1. When extracting files/installing freesurfer tar.gz, would the update
override the 5.2 files if I want to keep the same path, or I have to delete
5.2 first? I obviously want to preserve '/subjects' data already processed.
2. Freesurfer distribution contains some CUDA files. On the computer, I
have CUDA 5.5 version. Do you see any incompatibility issues (5.2 worked ok
in this respect).
3. Could you send me the T1 and T2 space MR protocols you use for
assistance with getting pial recon optimized.

Thank you,

Octavian
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[Freesurfer] v 5.3 pial- FLAIR vs T2

[octavian lie]

Dear All,

Among T2 FLAIR, eT2W FLAIR sense, T2, which sequence should be preferably
used as auxiliary for pial definition?
Does Freesurfer take care of coregistration between these and the MPRAGE?
What would be the command line (Linux Ubuntu) if I want to use SPM
generated nifti DICOM concatenations for the T2 or FLAIR, instead of native
DICOMs?
Thank you,

Octavian
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Re: [Freesurfer] volume of interest

[octavian lie]

Dear Douglas,

Thank you very much for your input.

1. I generated the ind matrix as per your script, but what I wanted is to
get a matrix with the RAS coordinates for the pixels indexed in ind. Is
there a way to do this?

Thank you,

Octavian
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[Freesurfer] volume of interest

[octavian lie]

Dear All,

I have created a volume of interest in itksnap and imported it in FS
as a .mgz volume filled binary mask. How can I:
1. export it from FS in matlab and generate a .mat array containing
only the volume pixels within the volume (intensity 1) ?

2. Is there a way to generate a 3D surface mesh of the boundary of the
volume of interest, as, for example, with the brain pial surface? If
not, is there a way to import into FS formats such as VTK, STL or BYU
meshes?

Thank you,

Octavian
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[Freesurfer] Import % crop

[octavian lie]

Dear All,

Excuse the basic nature of these quetions. I coregistered 2 analyze volumes
in SPM (pre and post resection MR scans for same patient) with cost
function masking. I imported the preresection scan in Freesurfer, and
processed it with recon -all.
1) What transform matrices should I multiply the postresection scan to get
it in the FS space in alignment with the processed preresection MR, and
where do I find them?
2) Once in FS, how do I crop/mask the posteresection volume using
saggittal, coronal or axial planes of my choosing? (I am interested in
generating a small cube containing the posteresection volume, then
extracting the postresection volume itself by intensity threshold (CSF vs
surronding cavity wall brain) and masking with preresection MR pial surface
laterally).

Please advise,

Octavian.
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Re: [Freesurfer] VOI

[octavian lie]

Dear Bruce,
>>
>
If I use freeview slice by slice to mark the resection boundaries and I
mark a set of vertices on each slide, how should I save those? Do I have to
create a set of labels, each on one slide, and then combine them, or how?
I thank you for your thoughts,
Octavian.



>
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> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
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> HelpLine at
> http://www.partners.org/**complianceline.
>  If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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[Freesurfer] VOI

[octavian lie]

Dear All,
I have 2 coregistered MR volume (pre and postresective MRI) sets
for several epilepsy patients. I need to extract the resection volume (VOI=
pre - postresection volume) as a set of voxel coordinates. Can I do this in
freesurfer? Ideally I would avoid manual delineation slice by slice as in
MRImicro and if possible I would do it automatically by thresholding, for
example. If not, manual is fine if it can be done in FS.
Please advise.
Thank you,
Octavian.
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Re: [Freesurfer] Cropping/slicing surfaces

[octavian lie]

Dear Bruce,

Thank you for your assist.
I see the difference between patch and surface, but I would need to get he
cut surface in matlab. I do not know how to set the ripflag=1 for x<0.
Here is the code I use to upload surfaces in Matlab:

function [vertex_coords, faces] = read_surf(fname)

%QUAD_FILE_MAGIC_NUMBER =  (-1 & 0x00ff) ;
%NEW_QUAD_FILE_MAGIC_NUMBER =  (-3 & 0x00ff) ;
TRIANGLE_FILE_MAGIC_NUMBER =  16777214 ;
QUAD_FILE_MAGIC_NUMBER =  16777215 ;
fid = fopen(fname, 'rb', 'b') ;
if (fid < 0)
str = sprintf('could not open curvature file %s.', fname) ;
error(str) ;

end
magic = fread3(fid) ;
if (magic == QUAD_FILE_MAGIC_NUMBER)
vnum = fread3(fid) ; %number of vertices
fnum = fread3(fid) ; %number of faces
vertex_coords = fread(fid, vnum*3, 'int16') ./ 100 ;
if (nargout > 1)
 for i=1:fnum
 for n=1:4
 faces(i,n) = fread3(fid) ;
end
end
end
elseif (magic == TRIANGLE_FILE_MAGIC_NUMBER)
  fgets(fid) ;
fgets(fid) ;
vnum = fread(fid, 1, 'int32') ; %number of vertices
fnum = fread(fid, 1, 'int32') ; %number of faces
vertex_coords = fread(fid, vnum*3, 'float32') + 1 ;
vertex_coords = reshape(vertex_coords, 3, vnum)';
faces = fread(fid, fnum*3, 'int32') + 1 ;
faces = reshape(faces, 3, fnum)' ;
end
fclose(fid) ;


Can something be done with this, or do I need to transform the surface
before importing it into matlab?

Thank you for your help
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Re: [Freesurfer] Cropping/slicing surfaces

[octavian lie]

Dear Bruce,
One last question. I saved the cut surface as rh.inner-skull-surface
(original was rh.sub_inner_skull_surface) as a patch, but when trying to
see it in tksurfer, I get the following error message:

tksurfer sub rh inner-skull-surface
subject is sub
hemi is rh
surface is inner-skull-surface
surfer: current subjects dir: /usr/local/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /home/ovl
checking for nofix files in 'inner-skull-surface'
Reading image info (/usr/local/freesurfer/subjects/graff)
Reading /usr/local/freesurfer/subjects/graff/mri/orig.mgz
surfer: Reading header info from
/usr/local/freesurfer/subjects/graff/mri/orig.mgz
mrisFindNeighbors:
/usr/local/freesurfer/subjects/graff/surf/rh.inner-skull-surface:
face[0].v[0] = 0, but face 0 not in vertex 0 face list

What should I do so that the cut surface is interpreted as surface for
import in matlab and electrode projection?

Octavian
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Re: [Freesurfer] Cropping/slicing surfaces

[octavian lie]

Thank you, Bruce. Is seems that the cut works well in tksurfer, however I
am unable to save the cut surface, if I use save or save as, it saves the
original (whole) surface. What should I do?
Octavian.

On Thu, Nov 1, 2012 at 11:49 AM, Bruce Fischl wrote:

> the easiest thing would be to copy it into surface as lh.bem then run
> tksurfer on it
>
> On Thu, 1 Nov 2012, octavian lie wrote:
>
>  Thank you for your quick prompt, how do I pull the inner skull surface
>> into tksurfer, given it is in /bem and not in /surf, and
>> does not have a lh or rh option?
>> Octavian
>>
>> On Thu, Nov 1, 2012 at 11:41 AM, Bruce Fischl 
>> wrote:
>>   Hi Octavian
>>
>>   sure, define a sagittal cutting plane in tksurfer, or in matlab set
>> ripflag=1 for all vertices with the x coord > 0
>>       (or < 0)
>>
>>   cheers
>>   Bruce
>>   On Thu, 1 Nov 2012, octavian lie wrote:
>>
>> Dear all,
>>
>> Is there a way to crop a surface in FS, freeview or matlab? I
>> have the inner_skull_surface in BEM
>> folder, and I want to see just
>> the right half, akin to cropping along the A (RAS) axis from
>> the left. This is in order to visualize the
>> inside of the surface
>> with some electrode applications. Also, if the surface can be
>> created in MNE just on the right side that
>> will solve it.
>> Help much appreciated,
>> Octavian Lie.
>>
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
>>  If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
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[Freesurfer] Cropping/slicing surfaces

[octavian lie]

Dear all,

Is there a way to crop a surface in FS, freeview or matlab? I have the
inner_skull_surface in BEM folder, and I want to see just the right half,
akin to cropping along the A (RAS) axis from the left. This is in order to
visualize the inside of the surface with some electrode applications. Also,
if the surface can be created in MNE just on the right side that will solve
it.
Help much appreciated,
Octavian Lie.
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Re: [Freesurfer] coordinate transform

[octavian lie]

Sorry,
I do not seem to see the light.
I have a point in volume index coordinates [128.9 172 62.9 1] and need to
obtain the surface/vertex RAS coordinates (not volume RAS).

matlab path
 /usr/local/freesurfer/subjects/subjid/mri
if I type
tkrRAS = Torig*[128.9 172 62.9 1]'

it tells me Torig undefined function or variable

If I try to define it with Torig: mri_info --vox2ras-tkr orig.mgz, it does
not recognize mri_info


Nothing happens if I work from the freesurfer command window:

   - Torig = mri_info --vox2ras-tkr orig.mgz


   - tkrRAS = Torig*[128.9 172 62.9 1]'

I do not want to use tkmedit/tksurfer clicking since I plan doing this
transform for  a list of points.

I know this is boringly basic but I am stuck, please advise.


Octavian

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[Freesurfer] CT transform to MNI152 2mm

[octavian lie]

Dear all,

I need to coregister a set of volumes/patient (brain.mgz,
?dpial.ribbon.mgz, and rCT head (CT head already coregistered with the
T1.mgz in SPM and imported in FS) to MNI152 2mm space.
After I coregister the brain.mgz to MNI152, how do I apply the generated
register.dat matix to the ?dpial.ribbon.mgz and rCT head volumes for
normalization?
Also, that all patient volumes are 1mm and MNI template is 2 mm (I need
this specific one) is an issue during normalization?

Thank you,

Octavian Lie.
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[Freesurfer] mris_pmake options

[octavian lie]

Dear all,

I need to measure the distance between 2 points on the same hemisphere for
subject A, in the common surface space as I have to compare it with the
distance between other 2 points for subjects B, C...
I used

mris_pmake --subject A --hemi rh --surface0 sphere.reg --curv0 sulc --curv1
sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs
startVertex:1,endVertex:2
Questions:
1. Is the calculated path the geodesic, in this case
spherical, measure that can be directly compared with that from another
subject, or not?
2. How could I compare the distance on the pial surface  of subject 1
(vertex 1-vertex 2) to subject 2 (vertex 1 to2). Is changing
--surface0 argument to pial enough? (In the Recon-all Dev table, sphere.reg
is an imput to generating label/?h.aparc.annot, which in turn is used to
generate ?h.pial surfaces, does that mean that pial surfaces from 2
subjects are already registered?)
3. I do not understand the choice of defaults for  --surface0 (inflated) ,
--surface1 (smoothwm), curve 0 and 1. This is not surprising, since I do
not have the math expression for the cost function available; just
wondering, what is the reason to have inlated as the default for surface 0?
Do I need to change any of the auxilliary terms used above with sphere.reg
to accomplish what I want to accomplish?
4. Last, is there a way to mark the vertices for these geodesic path on the
main surface used in order to use then for label creation?

Your insight is very important,
thank you,
Octavian.
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Re: [Freesurfer] Lesioned brain (surface) registration to fs average

[octavian lie]

Actually, the white matter is affected too within the resection bed.

Just to make sure, using mri_label2label with surface option to pass a
label from subject 1 to subject 2 is equivalent to registering that label
to fsaverage via sphere.reg for that subject, then transferring the label
from fs average to subject 2 via sphere.reg for subject 2. I assume I can
use it to transfer the label to fsaverage as well; is it better or
same/equivalent to use mri_surf2surf vs mri_label2label to transfer a label
from one subject to another

Thank you very much,

Octavian.
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[Freesurfer] Lesioned brain (surface) registration to fs average

[octavian lie]

Dear all,

I need to mark the cortical extent of a lesion (intersection of the lesion
and pial surface, where "lesion" represent a epilepsy related resection).
After the pial labeling of the resection, I need to register the labeled
surface to the fsaverage.
I completed recon-all routine on the postop T1, and went nicely, corrected
pial surface in a few places.
Question: what is the best way to mark the pial extent of a resection? Is
there a way to accurately register the lesioned pia to the fsaverage,
potentially by masking the resection ROI?
Thank you for your insight,

Octavian.
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Re: [Freesurfer] coordinate transform

[octavian lie]

Dear all,
I need to transform my electrode FS volume index coordinates stored in a
.mat file in surface RAS coordinates. Do you know of any matlab code that
could be shared to accomplish this and generate another .mat with RAS
coordinates?
Thank you,
Octavian Lie.

*To follow up and simplify for  a single electrode location,  *
**
*What I need to do is for each electrode (already localized/ projected onto
the surface) to transform its volume volume index coordinate to a vertex
RAS (maybe via the closest vertex volume coordinates), then to transform
these vertex RAS coordinates to fsaverage template coordinate.*
*I then need to calculate the geodesic and euclidean distance between the
electrode location and another selected surface vertex, say (a,b,c).*
*Thank you for your insight.*
**
*Octavian Lie.*
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[Freesurfer] coordinate transform

[octavian lie]

Dear all,

I need to transform my electrode FS volume index coordinates stored in a
.mat file (see attached) in surface RAS coordinates. Do you know of any
matlab code that could be shared to accomplish this and generate another
.mat with RAS coordinates?

Thank you,

Octavian Lie.


trodes.mat
Description: Binary data
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[Freesurfer] Pial error on lesioned brain

[octavian lie]

Dear All,
>
> I processed a MR brain after temporal lobe resection. While brainmask.mgz,
> and brain.mgz include the temporal remnant (correctly), the calculated pial
> surface excludes it (see attached). How, and at what step can I edit the
> image so that the pial surface (red line) is inclusive of the postop
> temporal lobe? Again, this is not a problem with skull extraction, and
> overall I am happy with brainmask.mgz as is, but not with subsequent pial
> calculations. Setting the volume brush to clone from brainmask.mgz the
> temporal remnant does not seem to help, I may be doing smth wrong.
> Please advise, thank you very much.
>
> Octavian.
>
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[Freesurfer] Output volume along with its calculated pia

[octavian lie]

Dear All,

I am increasingly fascinated by freesurfer.
Here is a rookie issue: I use a source imaging program that is rather
simple-minded in its MRI processing steps. To be able to use the inverse
solution tools of that program, I need to use 2 volumes:
- a head MRI to be used to electrode coregistration
- a skull-stripped brain MR without cerebellum, including both the gray and
white matter; the program needs to perform its own white matter extraction
to generate the gray matter volume to be used as source space.
- both MRs have to be subject to the same transforms, if any, and have to
have the same origin and coordinate systems (like real head/brain pairs).

So first, I am in the search of the "best" brain extraction possible, with
as little dura included as possible. Besides trying to implement Andre's
dura protocols, and editing the pial surface for brainmask.mgz, then
running the rest of the recon-all steps, I need to be able to export in
nii.gz format a volume having its pial surface as calculated by freesurfer.
When exporting brain.finalsurfs.mgz with mri_convert, it looks that the
calculated pial surface as visualized with tkmedit subjid
brain.finalsurfs.mgz -surfs is ignored in the nii.gz file. When the output
nii volume is imported  in programs such as Bioimage Suite, I essentially
see what looks like the outside (surface) brainmask.mgz volume as in
tekmedit but not accounting for the calculated pial surface. How can I
export brain.finalsurfs.mgz with its calculated pial surface as a nii
volume? In other words, I would need a ribbon.mgz type volume to include
the white matter on the inside. I suppose it comes down to adding options
to the mri_convert brain.finalsurfs.mgz step after surfaces have been
generated, but I would need some guidance
Please advise.


Octavian.
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[Freesurfer] Coordinates of output files

[octavian lie]

Dear All,

I am using a pipeline for electrode coregistration including freesurfer for
pial surface generation, run by default recon-all -all and mris_volmask
with --save_distance option. The FS files ?h.dpial.ribbon.mgz are the sole
FS output. They are converted in the pipeline to nii.gz files using the
mri_convert with no specific flags. Question, what coordinate
system is used in the converted nii.gz file: a native/scan system, FS
system, talairach system (after several recon-all steps of talairach
transformation), or NIFTI system? Is there a way to call a command to
confirm the exact system used?
Thank you,


Octavian.
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Re: [Freesurfer] ?h.dpial.ribbon.mgz not found

[octavian lie]

Dear all,

to follow up on my prior message below, I must say that I called the
recon-all -autorecon-all command remotely through a automatic  matlab
routine in which freesurfer is one leg, with the command nohup. For some
reason, when doing this, the step mris_volmask was run without the option
--save_distance hence no ?h.dpial.ribbon.mgz fille was created. To fix
this, I manually entered the following command in the linux terminal:
mris_volmask--label_left_white 2 --label_left_ribbon 3 --label_right_white
41 --label_right_ribbon 42 --save_ribbon --save_distance SUB002, which
created the output files needed.

Now, do you know why running recon-all -all remotely would exclude the
option --save_distance for mris_volmask. Is there any way to fix this in
the freesurfer itself, so that I do not have to change the matlab code?

Thank you, also see my message below.
Octavian.
On Sat, Feb 25, 2012 at 6:46 PM, octavian lie wrote:

> Dear Bruce & FreeSurfers,
>
> I ran freesurfer (86x64_64 centos version 5.1.0) on my new linux box
> (Ubuntu 11.10 64 bit, NVIDIA GEforce GTX 580, no CUDA for now) using
> recon-all -all; it went on for 8 hours, I got the message (Recon complete
> without errors) in the output.txt file in my subject directory. However,
> when trying to use mri_convert or tkmedit to see the lh.dpial.ribbon.mgz,
> there was an error (could not open file). I searched for the file in all
> the /mri folder and the whole file system on my box, could not find it. I
> found lh.ribbon.mgz, rh.ribbon.mgz, and ribbon.mgz, but not the
> dpial.ribbon.mgz file or any other ?.ribbon.mgz variety.
> I appreciate your suggestions.
>
> Octavian.
>
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[Freesurfer] ?h.dpial.ribbon.mgz not found

[octavian lie]

Dear Bruce & FreeSurfers,

I ran freesurfer (86x64_64 centos version 5.1.0) on my new linux box
(Ubuntu 11.10 64 bit, NVIDIA GEforce GTX 580, no CUDA for now) using
recon-all -all; it went on for 8 hours, I got the message (Recon complete
without errors) in the log.txt file in my subject directory. However, when
trying to use mri_convert or tkmedit to see the lh.dpial.ribbon.mgz, there
was an error (could not open file). I searched for the file in all the /mri
folder and the whole file system on my box, could not find it. I found
lh.ribbon.mgz, rh.ribbon.mgz, and ribbon.mgz, but not the dpial.ribbon.mgz
file or any other ?.ribbon.mgz variety.
I appreciate your suggestions.

Octavian.
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Re: [Freesurfer] Dura too bright/thick: brain extraction

[octavian lie]

Thank you.

Unfortunately, we use a Phillips scanner for 3T scans: MPRAGE T1 TR
9.89; TE 4.60. If you have any suggestions, including which of the
protocols comes closest, let mw know.
Best,
Octavian

On 1/31/12, Andre van der Kouwe  wrote:
> Do you have a Siemens scanner?
>
> You can compare your protocols with the examples at
> www.nmr.mgh.harvard.edu/~andre.
>
> On Tue, 31 Jan 2012, Bruce Fischl wrote:
>
>> Hi Octavian
>>
>> what kind of scanner are you using? Andre van der Kouwe and Dylan Tisdall
>> (ccd) have developed a multi-echo mprage that allows one to identify dura
>> by
>> it's short T2*. They might be able to give it to you depending on your
>> scanner and relationship with Siemens. Otherwise it can be difficult, as
>> lenghtening your TE to reduce the dura signal also reduced gray/white
>> contrast.
>>
>> cheers
>> Bruce
>> On Tue, 31 Jan 2012, octavian lie wrote:
>>
>>>  Dear All,
>>>
>>>  I am trying to perform brain extraction on T1 3D images, however the
>>>  dura appears too bright and thick compared to the underlying gray
>>>  matter. It seems that I have a hard time stripping the dura away. Do
>>>  you have any suggestions in terms of optimizing freesurfer parameters
>>>  to help with this problem, or alternatively, do you suggest a specific
>>>  T1 protocol (TE/TR) to dim the dura a bit?
>>>  Thank you,
>>>
>>>
>>>  Octavian Lie.
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>>>
>>>
>>>
>>
>>
>>
>
>
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[Freesurfer] Dura too bright/thick: brain extraction

[octavian lie]

Dear All,

I am trying to perform brain extraction on T1 3D images, however the
dura appears too bright and thick compared to the underlying gray
matter. It seems that I have a hard time stripping the dura away. Do
you have any suggestions in terms of optimizing freesurfer parameters
to help with this problem, or alternatively, do you suggest a specific
T1 protocol (TE/TR) to dim the dura a bit?
Thank you,


Octavian Lie.
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Re: [Freesurfer] Ubuntu 11.10 64 bit

[octavian lie]

Thank you for the info, can you share what freesurfer version you have that
happens to work well with ubuntu 11.10?
Octavian
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[Freesurfer] Ubuntu 11.10 64 bit

[octavian lie]

Dear All,
 I am in the process of getting a powerful linux laptop to run Freesurfer.
Can I run Freesurfer on a 11.10 version of Ubuntu 64 bit ? Are there any
incompatibilities between the latest Freesurfer version and Ubuntu? Is
there any configuration issues and solution particular to my situation that
you can comment on?
 Thank you,
 
Octavian.mailto:octavian.octavian@gmail.com>
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