[Freesurfer] mapping from Desikan-Killiany regions to resting state networks

[Krieger, Donald N.]

External Email - Use Caution

Dear list,

I would like to find a reasonably good mapping from Desiken-Killiani ROIs and 
as many of the resting state networks as makes sense, e.g. salience, visual, 
etc.
I have made a start using the network <> ROI mapping in the Conn Toolbox 
but I think there is likely a better starting place.
Any direction would be most welcome.

Thanks - Don

Don Krieger, PhD
Research Scientist
Department of Neurological Surgery
University of Pittsburgh

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Re: [Freesurfer] mri_label2label: one-to-one for subjectNo --> ico

[Krieger, Donald N.]

External Email - Use Caution

Hi Doug,

I’m trying to do two different things but let’s focus on the one which does not 
involve dilation.

I have a pair of vertices in a “white” label.
I want to compute the shortest distance from one vertex to the other along the 
“white” surface.
My approach is to project the pair onto the icosahedron, identify the great 
circle which connect them there, interpolate a bunch of points in the 
intersection between the great circle arc that connects them, project all those 
back to the original “white” label, and then walk from one vertex to the next 
to count the total distance between the original pair.

I can do the projection from “white” label to ico to “white” label as follows:
Original “white” label --> ico
mri_label2label --srcsubject 174 --srclabel lh.pairsets.label --trgsubject ico 
--trgicoorder 7 --trglabel /dev/shm/ico_1.label --regmethod surface --hemi lh
I add in the great circle interpolated points to ico_1.label to create 
ico_2.label and then
do the projection back:
mri_label2label --srcsubject ico --srclabel /dev/shm/ico_2.label --trgsubject 
174 --srcicoorder 7 --trglabel /dev/shm/lh.pairpaths.label --regmethod surface 
--hemi lh

There are two problems that I see.

(1)Notice that I need to do this for many pairs at a time because 
mri_label2label startup is slow. But to do that, I need to be able to identify 
the points in ico_1.label, i.e. in the icosahedron to which each of the 
original vertices was projected and of course vica versa for the points 
projected back from the icosahedron into lh.pairpaths.label. You suggested 
using mris_apply_reg –nnf to make the projections one-to-one which makes sense 
but I don’t see the functionality in that tool that is needed to do the 
projections to and from the icosahedron or to do so with anything but a volume 
file. Perhaps I’m missing something.

(2)mri_label2label appears to rely on the index numbers in column 1 of the 
label file. I do not, however, understand the correspondence between the index 
numbers in ico_1.label and their relationship to the index numbers in 
/usr/local/pkg/freesurfer//lib/bem/ic7.tri which looks like a label file but 
the index numbers with corresponding xyz coordinates for the vertices in 
ico_1.label don’t match up with those in ic7.tri, even when multiplied by 100 
The thing is that when I interpolate along the great circle route between a 
pair of vertices in the icosahedron projection, it looks like I need to select 
points in ic7.tri with the correct index numbers to get the right answer when I 
project the icosahedron vertices back to the “white” label.

I hope these questions are clear.

Thanks – Don
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Friday, December 10, 2021 6:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_label2label: one-to-one for subjectNo --> ico

Don, can you send your command line? If you are using surface-based 
registration, then the origin should not matter. You are right that there is 
not a one-to-one correspondence. The way it works  is that it starts on the 
target surface, goes through all the vertices and finds the closest vertex in 
the source and maps the value. At this point, each target only has one source, 
but each source may have multiple targets. By default, it then goes through 
another loop where it finds all the source vertices that have not been mapped, 
finds the closest target vertex, and  maps the source to that target 
(eventually taking the mean or sum of all the sources that map to a given 
target). If it is the 2nd stage that is giving you problems, then you can turn 
it off in mris_apply_reg with --nnf (stands for "nearest-neighbor-forward", vs 
the default nnfr where r=reverse).

On 12/3/2021 8:41 AM, Krieger, Donald N. wrote:

External Email - Use Caution
Dear Bruce, Doug, and everyone,


  1.  I am projecting labels from a subject’s labels onto the icosahedron and 
note that the mapping is not one-to-one. Because of this, I cannot tell which 
subject vertex maps to which icosahedron vertex which I need to able to do. 
What am I missing here?
  2.  Just double-checking something simple – The center of the icosahedron is 
as the origin, i.e. 0,0,0, yes?

Thanks – Don




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Re: [Freesurfer] mri_label2label: one-to-one for subjectNo --> ico

[Krieger, Donald N.]

External Email - Use Caution

Thanks for getting back on this, Doug.
I want to try a few things and make sure I understand what you’ve written 
before I get back to you.

Best – Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Friday, December 10, 2021 6:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_label2label: one-to-one for subjectNo --> ico

Don, can you send your command line? If you are using surface-based 
registration, then the origin should not matter. You are right that there is 
not a one-to-one correspondence. The way it works  is that it starts on the 
target surface, goes through all the vertices and finds the closest vertex in 
the source and maps the value. At this point, each target only has one source, 
but each source may have multiple targets. By default, it then goes through 
another loop where it finds all the source vertices that have not been mapped, 
finds the closest target vertex, and  maps the source to that target 
(eventually taking the mean or sum of all the sources that map to a given 
target). If it is the 2nd stage that is giving you problems, then you can turn 
it off in mris_apply_reg with --nnf (stands for "nearest-neighbor-forward", vs 
the default nnfr where r=reverse).

On 12/3/2021 8:41 AM, Krieger, Donald N. wrote:

External Email - Use Caution
Dear Bruce, Doug, and everyone,


  1.  I am projecting labels from a subject’s labels onto the icosahedron and 
note that the mapping is not one-to-one. Because of this, I cannot tell which 
subject vertex maps to which icosahedron vertex which I need to able to do. 
What am I missing here?
  2.  Just double-checking something simple – The center of the icosahedron is 
as the origin, i.e. 0,0,0, yes?

Thanks – Don




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[Freesurfer] mri_label2label: one-to-one for subjectNo --> ico

[Krieger, Donald N.]

External Email - Use Caution

Dear Bruce, Doug, and everyone,


  1.  I am projecting labels from a subject's labels onto the icosahedron and 
note that the mapping is not one-to-one. Because of this, I cannot tell which 
subject vertex maps to which icosahedron vertex which I need to able to do. 
What am I missing here?
  2.  Just double-checking something simple - The center of the icosahedron is 
as the origin, i.e. 0,0,0, yes?

Thanks - Don

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Re: [Freesurfer] shortest distance between two points along the gray/white boundary

[Krieger, Donald N.]

External Email - Use Caution

Thanks, Bruce, and thanks for getting back so quickly.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fischl, Bruce
Sent: Wednesday, July 21, 2021 11:08 AM
To: 'freesurfer@nmr.mgh.harvard.edu' 
Subject: Re: [Freesurfer] shortest distance between two points along the 
gray/white boundary

Hi Don

By far the easiest way to do this is to find the locations of the points on the 
sphere then compute the length of the great circle arc connecting them, then 
correct by the ratio of the sqrt of the areas of the two surfaces.

Alternatively I think Rudolph may have had some tools for computing actual 
geodesics (the procedure about will give you like a 10% error)

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Krieger, Donald N.
Sent: Wednesday, July 21, 2021 10:53 AM
To: 'freesurfer@nmr.mgh.harvard.edu' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] shortest distance between two points along the gray/white 
boundary


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Dear experts,

I would like to compute the shortest distance along the gray/white boundary 
between two points on the boundary, i.e. between points with "white" 
parcellation regions. The distance need not be guaranteed to be minimized and 
the path need not be unique. Can you suggest an approach using the freesurfer 
tools?

Thanks - Don

Department of Neurological Surgery
University of Pittsburgh

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[Freesurfer] shortest distance between two points along the gray/white boundary

[Krieger, Donald N.]

External Email - Use Caution

Dear experts,

I would like to compute the shortest distance along the gray/white boundary 
between two points on the boundary, i.e. between points with "white" 
parcellation regions. The distance need not be guaranteed to be minimized and 
the path need not be unique. Can you suggest an approach using the freesurfer 
tools?

Thanks - Don

Department of Neurological Surgery
University of Pittsburgh

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Re: [Freesurfer] cortical thickness values for each point in a ctx label file

[Krieger, Donald N.]

External Email - Use Caution

It looks like your first answer, i.e. use of mri_annotation2label to extract 
pial labels almost gets me there. I see that the pial and white labels have 
exactly the same number and values for their indices. Does this mean I can use 
the distance between the white and pial vertex with the same label as a 
cortical thickness?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Krieger, Donald N.
Sent: Thursday, February 11, 2021 1:16 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] cortical thickness values for each point in a ctx 
label file


External Email - Use Caution
Thanks for getting back so quickly, Doug.
Creating pial label files will enable me to write something which does what I 
want.

What I want to do is generate a list of cortical thickness values, one for each 
vertex in a ctx label file. The main question is whether something to do this 
has already been implemented in freesurfer. If not, I will generate pial label 
files and then for each vertex in a ctx label file, I will find the nearest 
points in that ROI's pial and white label files and use the sum of the two 
distances as the cortical thickness.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Douglas N. Greve
Sent: Thursday, February 11, 2021 1:04 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] cortical thickness values for each point in a ctx 
label file

Not sure what you mean as the pial files are surfaces not labels or 
annotations. If you want to extract labels from the annotations you can use 
mri_annotation2label
On 2/11/2021 12:55 PM, Krieger, Donald N. wrote:

External Email - Use Caution
Dear freesurfer group,

I wish to measure a cortical thickness value for each entry in a label file, 
e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label .
Is there a function in the freesurfer distribution which includes this 
capability?
Also, is there a function in the distribution that produces regional label 
files from the surf/[lr]h.pial files?

Thanks - Don

[cid:image001.jpg@01D70079.6E02F790]
Don Krieger, Ph.D.
Research Scientist
Department of Neurological Surgery
University of Pittsburgh



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Re: [Freesurfer] cortical thickness values for each point in a ctx label file

[Krieger, Donald N.]

External Email - Use Caution

Thanks for getting back so quickly, Doug.
Creating pial label files will enable me to write something which does what I 
want.

What I want to do is generate a list of cortical thickness values, one for each 
vertex in a ctx label file. The main question is whether something to do this 
has already been implemented in freesurfer. If not, I will generate pial label 
files and then for each vertex in a ctx label file, I will find the nearest 
points in that ROI's pial and white label files and use the sum of the two 
distances as the cortical thickness.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Thursday, February 11, 2021 1:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical thickness values for each point in a ctx 
label file

Not sure what you mean as the pial files are surfaces not labels or 
annotations. If you want to extract labels from the annotations you can use 
mri_annotation2label
On 2/11/2021 12:55 PM, Krieger, Donald N. wrote:

External Email - Use Caution
Dear freesurfer group,

I wish to measure a cortical thickness value for each entry in a label file, 
e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label .
Is there a function in the freesurfer distribution which includes this 
capability?
Also, is there a function in the distribution that produces regional label 
files from the surf/[lr]h.pial files?

Thanks - Don

[cid:image001.jpg@01D70078.13992C80]
Don Krieger, Ph.D.
Research Scientist
Department of Neurological Surgery
University of Pittsburgh




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[Freesurfer] cortical thickness values for each point in a ctx label file

[Krieger, Donald N.]

External Email - Use Caution

Dear freesurfer group,

I wish to measure a cortical thickness value for each entry in a label file, 
e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label .
Is there a function in the freesurfer distribution which includes this 
capability?
Also, is there a function in the distribution that produces regional label 
files from the surf/[lr]h.pial files?

Thanks - Don

[cid:image003.jpg@01D70075.1EC687E0]
Don Krieger, Ph.D.
Research Scientist
Department of Neurological Surgery
University of Pittsburgh

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Re: [Freesurfer] tracula FA question - 2 cohorts/2 scanners

[Krieger, Donald N.]

External Email - Use Caution

Thanks for getting back on this.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Yendiki, Anastasia
Sent: Monday, October 21, 2019 10:25 PM
To: 'freesurfer@nmr.mgh.harvard.edu' 
Subject: Re: [Freesurfer] tracula FA question - 2 cohorts/2 scanners

Hi Don - Diffusivity and FA depend on the b-value. Even if you just scan a 
subject with multiple b-values on a single scanner, and you compute FA etc from 
each shell, you'll get different values in the same voxel. So this is unrelated 
to what tractography method you use, tracula or other. There is literature on 
harmonization of diffusion measures across scanners, you might want to look 
into that.

a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Monday, October 21, 2019 7:37 AM
To: 'freesurfer@nmr.mgh.harvard.edu' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] tracula FA question - 2 cohorts/2 scanners


External Email - Use Caution

I have tracula runs on two cohorts whose imaging was obtained on different 
scanners with slightly different beta's and other parameters.

Would the differences in the scanners and scanning parameters be expected to 
produce large cohort-wide differences in the FA's?

Can you point to a reference?



Thanks - Don




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[Freesurfer] tracula FA question - 2 cohorts/2 scanners

[Krieger, Donald N.]

External Email - Use Caution

I have tracula runs on two cohorts whose imaging was obtained on different 
scanners with slightly different beta's and other parameters.
Would the differences in the scanners and scanning parameters be expected to 
produce large cohort-wide differences in the FA's?
Can you point to a reference?

Thanks - Don


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Re: [Freesurfer] R: R: recon-all skull stripping

[Krieger, Donald N.]

External Email - Use Caution

Please pardon me for jumping in here.
I looks like recon-all -autorecon1 will do it, yes?

Best - Don 

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Wednesday, October 16, 2019 12:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] R: R: recon-all skull stripping

oh, sure, you can just run that part of recon-all. You don't need to rerun the 
whole thing cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote:

> 
> External Email - Use Caution
> 
> Hi Bruce,
> 
> what I mean is that, two of the main outputs of recon-all are T1.mgz 
> (which has the skull) and brain.mgz (which has been skull stripped). 
> For a group of patients, I lost the brain.mgz file and I still have 
> the T1.mgz. I was wondering if there was a way, given T1.mgz as input, 
> to get brain.mgz (avoiding the whole segmentation procedure again).
> 
> Thank you
> 
> BW
> Marianna
> 
> __
> __
> Da: freesurfer-boun...@nmr.mgh.harvard.edu
>  per conto di Bruce Fischl 
> 
> Inviato: mercoledì 16 ottobre 2019 17:40
> A: Freesurfer support list 
> Oggetto: Re: [Freesurfer] R: recon-all skull stripping Hi Marianna
> 
> I'm not sure what you mean by "replicate". The procedure should be the 
> same for all inputs unless you change something explicitly
> 
> cheers
> Bruce
> 
> On Wed, 16 Oct 2019,
> Inglese, Marianna wrote:
> 
> >
> > External Email - Use Caution
> >
> > Thank you Bruce.
> > I thought it was something similar to the FSL bet function, which 
> > extracts the brain using a fractional intensity threshold (0.5 for example).
> > So I guess I won't be able to replicate the same exact skull 
> > stripping of freesurfer's recon-all.
> >
> > BW
> > Marianna
> >
> >_
> >__
> _
> > Da: freesurfer-boun...@nmr.mgh.harvard.edu
> >  per conto di Bruce Fischl 
> > 
> > Inviato: mercoledì 16 ottobre 2019 17:23
> > A: Freesurfer support list 
> > Oggetto: Re: [Freesurfer] recon-all skull stripping Hi Marianna
> >
> > the skull stripping is a hybrid procedure that uses both a watershed 
> > algorithm and a deformable surface. There is no single intensity 
> > threshold in it. Maybe I'm misunderstanding your question? There are 
> > parameters you can change (for example the preflooding height), but 
> > there is no intensity thresholding
> >
> > cheers
> > Bruce
> >
> >
> > On Wed, 16 Oct 2019, Inglese, Marianna
> > wrote:
> >
> > >
> > > External Email - Use Caution
> > >
> > > To whom it may concern,
> > >
> > > I am using recon-all to segment many T1s. As I can see, one of the
> > automatic
> > > step performed by recon-all is the skull stripping. Would it be 
> > > possible
> > to
> > > know the threshold used for the stripping? I guess it is the same
> > threshold
> > > everytime. I would like to apply the skull stripping only on other 
> > > T1s
> and
> > > need to get the same result.
> > >
> > > Thank you very much for the help.
> > >
> > > Yours faithfully,
> > >
> > > Marianna Inglese
> > >
> > > Research fellow, Imperial College London Department of Surgery and 
> > > Cancer
> > >
> > >
> > >
> >
> >
> 
>


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Re: [Freesurfer] Tracula: Transform streamlines to T1 RAS coordinates

[Krieger, Donald N.]

External Email - Use Caution

Thanks for getting back so quickly, Anastasia.
I assume you are answering a question about what dmri_trk2trk is doing.
Could you please confirm?

Could you also please look at the sequence of transforms I am using and confirm 
that these are correct?
Transform from voxel (diffusion space) to RAS coordinates (mm) in the tkraster 
space:
 mri_info --vox2ras-tkr –in path.pd.nii.gz
Transform from tkraster space to RAS coordinates in the T1 space:
 mri_info –tkr-scanner –in 
$FREESURFER/subjects/SubNo/mri/orig.mgz

And that these are equivalent, please confirm:
Transform from voxel to RAS coordinates (mm), both in diffusion space:
  mri_info –vox2ras –in path.pd.nii.gz
Transform from diffusion space to tkraster space:
  mri_info –scanner2tkr –in path.pd.nii.gz
Transform from tkraster space to T1 scanner space:
  mri_info –scanner tkr2scanner –in 
$FREESURFER/subjects/SubNo/mri/orig.mgz

Thanks – Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Yendiki, Anastasia
Sent: Tuesday, January 22, 2019 8:46 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula: Transform streamlines to T1 RAS coordinates

Hi Donald - Both your input and output reference volume are in diffusion space 
and there is no transformation specified, so the output is also in diffusion 
space. These are voxel, not RAS, coordinates.

Best,
a.y


On Jan 22, 2019 7:14 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

External Email - Use Caution

I extract the streamlines for each tract from path.pd.trk to an ascii file and 
then wish to transform the coordinates to RAS T1 coordinates in millimeters.

My results are not correct.



Here is the extraction command I’m using. Is this correct? Perhaps I should be 
using orig.mgz as the outref volume? I do not understand –inref and --outref

dmri_trk2trk –in path.pd.trk –inref path.pd.nii.gz –outref path.pd.nii.gz 
–outasc test.streamlines



Given the above command, I am assuming that the output I’m getting is in the 
diffusion frame in voxel coordinates.

I extract 4x4 transforms and apply them in sequence; I append 1.0 to each 
3-vector before applying them of course.

Here is the most compact approach I’ve tried

1st transform: mri_info –in path.pd.nii.gz –vox2ras-tkr

2nd transform: mri_info –in orig.mgz –tkr2scanner



I’ve also tried this:

1st transform: mri_info –in path.pd.nii.gz –vox2ras

2nd transform: mri_info –in path.pd.nii.gz –scanner2tkr

3rd transform: mri_inf –in orig.mgz –tkr2scanner



I’ve tried some other sequence since I’m not sure what frame is the target 
output for the–vox2ras* transforms stored in path.pd.nii.gz .

Those are  the only transforms which contain the multiplication factors needed 
to get to millimeters from voxels.



Rather than continuing to fumble around, some direction from you who know would 
be very much appreciated.



Best - Don





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[Freesurfer] Tracula: Transform streamlines to T1 RAS coordinates

[Krieger, Donald N.]

External Email - Use Caution

I extract the streamlines for each tract from path.pd.trk to an ascii file and 
then wish to transform the coordinates to RAS T1 coordinates in millimeters.
My results are not correct.

Here is the extraction command I'm using. Is this correct? Perhaps I should be 
using orig.mgz as the outref volume? I do not understand -inref and --outref
dmri_trk2trk -in path.pd.trk -inref path.pd.nii.gz -outref path.pd.nii.gz 
-outasc test.streamlines

Given the above command, I am assuming that the output I'm getting is in the 
diffusion frame in voxel coordinates.
I extract 4x4 transforms and apply them in sequence; I append 1.0 to each 
3-vector before applying them of course.
Here is the most compact approach I've tried
1st transform: mri_info -in path.pd.nii.gz -vox2ras-tkr
2nd transform: mri_info -in orig.mgz -tkr2scanner

I've also tried this:
1st transform: mri_info -in path.pd.nii.gz -vox2ras
2nd transform: mri_info -in path.pd.nii.gz -scanner2tkr
3rd transform: mri_inf -in orig.mgz -tkr2scanner

I've tried some other sequence since I'm not sure what frame is the target 
output for the-vox2ras* transforms stored in path.pd.nii.gz .
Those are  the only transforms which contain the multiplication factors needed 
to get to millimeters from voxels.

Rather than continuing to fumble around, some direction from you who know would 
be very much appreciated.

Best - Don


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[Freesurfer] mni --> RAS T1

[Krieger, Donald N.]

External Email - Use Caution

Is there a 4x4 transformation somewhere to convert mni coordinates to RAS T1 
coordinates,
I.e. something comparable to the transforms provided by mri_info -tkrscanner

Thanks - Don


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Re: [Freesurfer] Notebook specification

[Krieger, Donald N.]

External Email - Use Caution

Dear Mustafa,

The Open Science Grid has freesurfer 5.3 and 6.0 installations and provides a 
simple user interface to upload scans, run freesurfer on them using OSG 
computing resources, and download the results. This facility was designed to 
meet the kinds of requirements you describe. Check out the link below to learn 
about it. If you decide to use it, the OSG has a good ticket system which 
provides help. 

https://support.opensciencegrid.org/support/solutions/articles/1208483-introduction-to-fsurf-and-freesurfer
 

Best - Don 

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ts...@rcmd.org
Sent: Sunday, December 30, 2018 10:20 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Notebook specification

External Email - Use Caution

One last thing I forgot: you could maybe check whether you can get access to 
some super computer. Maybe some university you know has one and you can request 
access (maybe even for free).

It's nice to have your own server, but access to a 2nd system is good to have 
as well.

Best,

Tim

> On December 30, 2018 at 9:46 AM mustafa amin  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear Freesurfer Members,
> 
> First I would like to introduce myself my name is Mustafa Amin, and I’m 
> planning to do a study to measure the volume of prefrontal cortex, 
> hippocampus, and ventricle of patients with schizophrenia comparing them with 
> control in Medan Indonesia. I read and saw information that freesurfer is 
> capable in doing the measurement, however I am still not sure about what kind 
> of notebook specification that I need to download and install it. For my 
> knowledge, this is the first study that will be done in Indonesia so every 
> explanation and further information about freesurfer and the notebook will 
> make me very grateful.
> 
> I’m thinking to buy an I5 intel core processor, with 8GB RAM, 1 TB HDD, and 
> full HD Nvidia MX130 2G8 specification notebook. If there is anyone in here 
> that can share the minimum requirements of the notebook, it will help me a 
> lot to choose which one to buy. Thank you in advance.
> 
> Yours faithfully,
> 
> Mustafa M. Amin
> Consultant Psychiatrist in Biological Psychiatry Department of 
> Psychiatry Faculty of Medicine Universitas Sumatera Utara
> 
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy 
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] mri_label2label dependencies

[Krieger, Donald N.]

External Email - Use Caution

Dear freesurfers,

I didn't see a response to this but I might have missed it.
In any case it looks like it's working ok.
I found an error in what I was doing which was confusing things.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Krieger, Donald N.
Sent: Wednesday, August 22, 2018 8:35 PM
To: 'freesurfer@nmr.mgh.harvard.edu' 
Subject: [Freesurfer] mri_label2label dependencies


External Email - Use Caution
Dear freesurfers,

I am using mri_label2label with -regmethod volume .
The only other switches I am using are minimal as you can see below.


The thing is that none of the freesurfer stuff is in the srcsubject's directory.
Why is there no error message?
Where is it getting the stuff below the line: Src2TrgVolReg: ---   ?

Actually, I just need to know what to put into those directories so this 
function will work properly.
I see from the documentation that I need mri/transforms/talairach.xfm in both 
the src and trg subject directories.
Is there anything else that needs to be there?

mri_label2label --trgsubject 174 --srcsubject subNo1 --trglabel 
/dev/shm/32089_labels --srclabel /dev/shm/32089_tmp0-2 --regmethod volume

srclabel = /dev/shm/32089_tmp0-2
srcsubject = subNo1
trgsubject = 174
trglabel = /dev/shm/32089_labels
regmethod = volume

usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/usr/local/pkg/freesurfer//subjects
FREESURFER_HOME /usr/local/pkg/freesurfer/
Loading source label.
Found 33 points in source label.
Starting volumetric mapping 33 points
Src2TrgVolReg: -
0.963  -0.002  -0.044   0.330;
0.034   0.930  -0.328  -0.544;
0.044   0.285   0.919   13.268;
0.000   0.000   0.000   1.000;
  0  55. 17. 23.52.2444 9.6043 41.6544
  1  47. 1. 39.43.8696 -10.7903 51.4429
  2  52. -4. 28.49.1826 -11.6594 40.1300
  3  55. 17. 16.52.5536 11.8998 35.2230
  4  50. -10. 23.47.4912 -15.6659 33.7380
Writing label file /dev/shm/32089_labels 33
mri_label2label: Done


Thanks - Don


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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] mri_label2label dependencies

[Krieger, Donald N.]

External Email - Use Caution

Dear freesurfers,

I am using mri_label2label with -regmethod volume .
The only other switches I am using are minimal as you can see below.


The thing is that none of the freesurfer stuff is in the srcsubject's directory.
Why is there no error message?
Where is it getting the stuff below the line: Src2TrgVolReg: ---   ?

Actually, I just need to know what to put into those directories so this 
function will work properly.
I see from the documentation that I need mri/transforms/talairach.xfm in both 
the src and trg subject directories.
Is there anything else that needs to be there?

mri_label2label --trgsubject 174 --srcsubject subNo1 --trglabel 
/dev/shm/32089_labels --srclabel /dev/shm/32089_tmp0-2 --regmethod volume

srclabel = /dev/shm/32089_tmp0-2
srcsubject = subNo1
trgsubject = 174
trglabel = /dev/shm/32089_labels
regmethod = volume

usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/usr/local/pkg/freesurfer//subjects
FREESURFER_HOME /usr/local/pkg/freesurfer/
Loading source label.
Found 33 points in source label.
Starting volumetric mapping 33 points
Src2TrgVolReg: -
0.963  -0.002  -0.044   0.330;
0.034   0.930  -0.328  -0.544;
0.044   0.285   0.919   13.268;
0.000   0.000   0.000   1.000;
  0  55. 17. 23.52.2444 9.6043 41.6544
  1  47. 1. 39.43.8696 -10.7903 51.4429
  2  52. -4. 28.49.1826 -11.6594 40.1300
  3  55. 17. 16.52.5536 11.8998 35.2230
  4  50. -10. 23.47.4912 -15.6659 33.7380
Writing label file /dev/shm/32089_labels 33
mri_label2label: Done


Thanks - Don


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Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Thanks for all the help and explanation, Anastasia.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 9:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


It would answer the question "if I were a voxel of the forceps major, how 
likely would I be to be in any particular location?"


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 2:10:50 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Ok - I have that sum.

For the forceps major, it's 111,685.

If I normalize by that, i.e. divide each voxel value by that, then I certainly 
get something that looks like a probability distribution since the sum of the 
normalized voxel entries over the entire volume is 1.0 as you had said in an 
earlier post.

But the maximum probability for any single voxel is 255/111685, i.e 0.0028.

Is that to be interpreted as the probability that the forceps major passes 
through a voxel with that value?

That is awfully low ... what am I missing?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 1:55 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - You would normalize these numbers by their sum, not by their maximum 
(i.e., not by 255).



a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 1:51:43 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi, Anastasia.



Yes, that makes it simpler.



I can see that each of the path.pd.nii.gz has a voxel entry for the same number 
of voxels. I'm looking at elmo.2008 for which that number is 1,294,336 which I 
presume is the volume of this person's brain as delivered by freesurfer.



Most of those voxels are set to 0.

I presume that means that the probability that the tract passes through that 
voxel is very near 0.0 .

For the forceps major, 7342 voxels have non-zero entries ranging from 1 to 255. 
Most of them are pretty low numbers so the average value for the 7342 non-zero 
voxels is about 16.

For a voxel that has an entry of 1, I presume the probability that the tract 
passes  through that voxel is near zero. For a voxel that has an entry of 127,  
is the probability that the tract passes through it 0.5 ?

And if the entry is 255, is the probability 1.0?



It's that mapping of voxel value to probability that I'm trying to get at. Or 
am I misunderstanding what the voxel value means?



Best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 12:46 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



The probability maps are independent for each tract. Each one just tells you 
how likely this one tract is to go through any given voxel, but it tells you 
nothing about other tracts. Does this make sense?



On Apr 11, 2018 12:00 PM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

Thanks for getting back, Anastasia.



I'm not suggesting that it should be done differently than it is.



I'm just trying to understand how the voxel values map to probability. That's 
why I described the wrong headed way I was thinking about it ... so you could 
tell me where I'm going wrong.







From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



This wouldn't work because these 18 tracts do not include all tracts in the 
brain.



On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond t

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Ok - I have that sum.
For the forceps major, it's 111,685.
If I normalize by that, i.e. divide each voxel value by that, then I certainly 
get something that looks like a probability distribution since the sum of the 
normalized voxel entries over the entire volume is 1.0 as you had said in an 
earlier post.
But the maximum probability for any single voxel is 255/111685, i.e 0.0028.
Is that to be interpreted as the probability that the forceps major passes 
through a voxel with that value?
That is awfully low ... what am I missing?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 1:55 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi Don - You would normalize these numbers by their sum, not by their maximum 
(i.e., not by 255).



a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 1:51:43 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi, Anastasia.



Yes, that makes it simpler.



I can see that each of the path.pd.nii.gz has a voxel entry for the same number 
of voxels. I'm looking at elmo.2008 for which that number is 1,294,336 which I 
presume is the volume of this person's brain as delivered by freesurfer.



Most of those voxels are set to 0.

I presume that means that the probability that the tract passes through that 
voxel is very near 0.0 .

For the forceps major, 7342 voxels have non-zero entries ranging from 1 to 255. 
Most of them are pretty low numbers so the average value for the 7342 non-zero 
voxels is about 16.

For a voxel that has an entry of 1, I presume the probability that the tract 
passes  through that voxel is near zero. For a voxel that has an entry of 127,  
is the probability that the tract passes through it 0.5 ?

And if the entry is 255, is the probability 1.0?



It's that mapping of voxel value to probability that I'm trying to get at. Or 
am I misunderstanding what the voxel value means?



Best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 12:46 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



The probability maps are independent for each tract. Each one just tells you 
how likely this one tract is to go through any given voxel, but it tells you 
nothing about other tracts. Does this make sense?



On Apr 11, 2018 12:00 PM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

Thanks for getting back, Anastasia.



I'm not suggesting that it should be done differently than it is.



I'm just trying to understand how the voxel values map to probability. That's 
why I described the wrong headed way I was thinking about it ... so you could 
tell me where I'm going wrong.







From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



This wouldn't work because these 18 tracts do not include all tracts in the 
brain.



On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:

I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.

I can see is likely wrong but for sure it's too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.

??



Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.

Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?

And how is the normalization mapped to probability?



Thanks - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



The volume would have to be normalized to a total sum of 

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Hi, Anastasia.

Yes, that makes it simpler.

I can see that each of the path.pd.nii.gz has a voxel entry for the same number 
of voxels. I'm looking at elmo.2008 for which that number is 1,294,336 which I 
presume is the volume of this person's brain as delivered by freesurfer.

Most of those voxels are set to 0.
I presume that means that the probability that the tract passes through that 
voxel is very near 0.0 .
For the forceps major, 7342 voxels have non-zero entries ranging from 1 to 255. 
Most of them are pretty low numbers so the average value for the 7342 non-zero 
voxels is about 16.
For a voxel that has an entry of 1, I presume the probability that the tract 
passes  through that voxel is near zero. For a voxel that has an entry of 127,  
is the probability that the tract passes through it 0.5 ?
And if the entry is 255, is the probability 1.0?

It's that mapping of voxel value to probability that I'm trying to get at. Or 
am I misunderstanding what the voxel value means?

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 12:46 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question

The probability maps are independent for each tract. Each one just tells you 
how likely this one tract is to go through any given voxel, but it tells you 
nothing about other tracts. Does this make sense?

On Apr 11, 2018 12:00 PM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
Thanks for getting back, Anastasia.

I'm not suggesting that it should be done differently than it is.

I'm just trying to understand how the voxel values map to probability. That's 
why I described the wrong headed way I was thinking about it ... so you could 
tell me where I'm going wrong.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question

This wouldn't work because these 18 tracts do not include all tracts in the 
brain.

On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.
I can see is likely wrong but for sure it's too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question


The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great - thanks - that's what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 - 1.0



Thanks again - best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, i

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Thanks, Anastasia.

I'll think about this and get back if I can't figure it out.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 12:46 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question

The probability maps are independent for each tract. Each one just tells you 
how likely this one tract is to go through any given voxel, but it tells you 
nothing about other tracts. Does this make sense?

On Apr 11, 2018 12:00 PM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
Thanks for getting back, Anastasia.

I'm not suggesting that it should be done differently than it is.

I'm just trying to understand how the voxel values map to probability. That's 
why I described the wrong headed way I was thinking about it ... so you could 
tell me where I'm going wrong.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question

This wouldn't work because these 18 tracts do not include all tracts in the 
brain.

On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.
I can see is likely wrong but for sure it's too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question


The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great - thanks - that's what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 - 1.0



Thanks again - best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.



More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni dire

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Thanks for getting back, Anastasia.

I'm not suggesting that it should be done differently than it is.

I'm just trying to understand how the voxel values map to probability. That's 
why I described the wrong headed way I was thinking about it ... so you could 
tell me where I'm going wrong.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 11:54 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question

This wouldn't work because these 18 tracts do not include all tracts in the 
brain.

On Apr 11, 2018 11:19 AM, "Krieger, Donald N." 
mailto:krieg...@upmc.edu>> wrote:
I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.
I can see is likely wrong but for sure it's too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question


The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great - thanks - that's what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 - 1.0



Thanks again - best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.



More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I 
haven't checked these lists to make sure they are actually what we need.



I haven't found documentation on these files nor do I see them in the tutorial 
directories for the three elmo's.

I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.



  1.  Are these the files that I'm looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?



It strikes me that maybe 

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

I was thinking that for a single voxel, the total of the values assigned to the 
voxel over all the tracts would have a maximum of 255 and that 255 would 
correspond to a probability of 1.0.
I can see is likely wrong but for sure it's too simple since each voxel could 
contain crossing fibers from several tracts; hence the total probability 
assigned to the voxel over all the tracts might be greater than 1.0.
??

Surely there is some normalization applied to the values assigned to the voxels 
so they fall between 0 and 255.
Does that normalization vary from one subject to the next and perhaps even from 
one tract to the next?
And how is the normalization mapped to probability?

Thanks - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:48 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


The volume would have to be normalized to a total sum of 1 for the voxel values 
to represent an actual distribution.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great - thanks - that's what I need.

I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.



I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 - 1.0



Thanks again - best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.



More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I 
haven't checked these lists to make sure they are actually what we need.



I haven't found documentation on these files nor do I see them in the tutorial 
directories for the three elmo's.

I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.



  1.  Are these the files that I'm looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?



It strikes me that maybe it is the streamlines which best define the tracts 
rather than these volumetric masks. I still do not thoroughly understand where 
in the processing sequence the streamlines get assigned to specific tracts. ??



Thanks - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - If the output files described here show up in the end, all is well:



https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.m

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Great - thanks - that's what I need.
I can use the probability for each pixel as a weight for the neuroelectric 
current count for that pixel to quantify the activity for the tract.

I assume that each voxel value maps directly to its probability, i.e. 0-255 --> 
0.0 - 1.0

Thanks again - best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, April 11, 2018 10:26 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi Don - No, dlabel/ contains files that are used in the pathway 
reconstruction, but the output of the reconstruction is saved in dpath/. 
There's a subdirectory in there for each pathway, and it contains a volume 
called path.pd.nii.gz. This is the probability that each voxel belongs to this 
pathway, in the subject's native diffusion space. As TRACULA is a probabilistic 
method, you get a probability associated with each voxel, rather than a set of 
voxel coordinates.


More info (potentially too much info) on TRACULA outputs:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles



Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:06:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Thanks for the additional information, Anastasia.

I will look for those files.



What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm 
looking for. They have names like

_AS_..nii.gz

where str1 = bbr or flt and

str2 = roi1 or roi2

I can extract the lists of coordinates from them with mri_cor2label although I 
haven't checked these lists to make sure they are actually what we need.



I haven't found documentation on these files nor do I see them in the tutorial 
directories for the three elmo's.

I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.



  1.  Are these the files that I'm looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?



It strikes me that maybe it is the streamlines which best define the tracts 
rather than these volumetric masks. I still do not thoroughly understand where 
in the processing sequence the streamlines get assigned to specific tracts. ??



Thanks - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - If the output files described here show up in the end, all is well:



https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 4:52:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Great - thanks.

It's running.

I see several warnings which I presume can be ignored:

hostname: Name or service not known



Best - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - See: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question



I am getting the following output with error on this command:



trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23



INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_HOME /media/portable/home/

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Thanks for the additional information, Anastasia.
I will look for those files.

What I am after is a list of xyz coordinates for each of the 18 tracts. I see 
masks in the trctrain/trc0xy/dlabel/mni directories which appear to be what I'm 
looking for. They have names like
_AS_..nii.gz
where str1 = bbr or flt and
str2 = roi1 or roi2
I can extract the lists of coordinates from them with mri_cor2label although I 
haven't checked these lists to make sure they are actually what we need.

I haven't found documentation on these files nor do I see them in the tutorial 
directories for the three elmo's.
I have bedbpostx running but do not expect it to produce them. I suppose it is 
trac-all -path which will do so but I thought I would ask my questions anyway.


  1.  Are these the files that I'm looking for?
  2.  If so, where can I find documentation?
  3.  What is the shortest path to generate them?

It strikes me that maybe it is the streamlines which best define the tracts 
rather than these volumetric masks. I still do not thoroughly understand where 
in the processing sequence the streamlines get assigned to specific tracts. ??

Thanks - Don


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 9:23 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi Don - If the output files described here show up in the end, all is well:



https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX



Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 4:52:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great - thanks.

It's running.

I see several warnings which I presume can be ignored:

hostname: Name or service not known



Best - Don





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - See: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question



I am getting the following output with error on this command:



trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23



INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: 
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected



I apologize for not finding the answer in the list archive.

It's probably there.



I'm running under ubuntu 14.04.



bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:



INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

subjectdir is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

Making bedpostx directory structure

Queuing preprocessing stages

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")

Queuing parallel processing stage

0 slices processed

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(&q

Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Great - thanks.
It's running.
I see several warnings which I presume can be ignored:
hostname: Name or service not known

Best - Don


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi Don - See: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html



Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question


I am getting the following output with error on this command:



trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23


INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: 
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected



I apologize for not finding the answer in the list archive.

It's probably there.



I'm running under ubuntu 14.04.



bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:


INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
subjectdir is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
Making bedpostx directory structure
Queuing preprocessing stages
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
Queuing parallel processing stage
0 slices processed
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
Queuing post processing stage
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: line 439: 26461 Terminated  
${subjdir}.bedpostX/monitor



Thanks - Don


___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 . 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.

[Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

I am getting the following output with error on this command:


trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23


INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: 
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected


I apologize for not finding the answer in the list archive.

It's probably there.


I'm running under ubuntu 14.04.


bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:


INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
subjectdir is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
Making bedpostx directory structure
Queuing preprocessing stages
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
Queuing parallel processing stage
0 slices processed
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
Queuing post processing stage
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: line 439: 26461 Terminated  
${subjdir}.bedpostX/monitor



Thanks - Don

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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 . 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.

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

[Krieger, Donald N.]

Dear Anastasia -

Yes, I noticed the added mri_convert capability in the release notes for 
Freesurfer 6.0 - that will save some work - thank you.

It sounds like there is no big down side to running tracula on a scan obtained 
with higher b-value. At present, I am primarily interested in using tracula to 
identify the ROIs at which each standard pathway terminates. Any additional 
thoughts would be welcome.

Thank you again for your help and time in getting me started on this.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Thursday, February 15, 2018 12:52 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI


Hi Donald - If you have recent dicoms from a standard manufacturer's sequence, 
then mri_convert should be able to read the b-values and gradient directions 
from the dicom header, in which case you don't have to provide them separately.



About which b-values to use - there's no short answer there. For sure the 
higher b-values contain additional info about white matter organization. But 
there are 2 "buts" here. First, with TRACULA you're not doing exploratory 
tractography, but instead you're trying to reconstruct some well-defined 
pathways, based on prior info on their anatomy. It's not clear that you need 
the additional info from the higher b-values for that. And TRACULA uses global 
tractography, where the usual issues of false positives/negatives that 
conventional streamline tractography gets into by either taking the wrong turn 
or terminating prematurely don't exactly apply. Second (or maybe third?), the 
ball-and-stick model may not fully take advantage of the additional info 
contained in those higher b-values, and it's not clear if there is a 
crossing-fiber model that does. We're doing post mortem validation studies at 
the moment to get to the bottom of these questions.



I hope I answered your question!


Anastasia.




From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Thursday, February 15, 2018 10:18:21 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI


Dear a.y.



Thanks for getting back.

I've set the wheels in motion to run tracula on the control scans that we have.

I found your notes in the diffusion_tutorial download for grabbing the bval and 
bvecs from each DTI slice which looks like the biggest difficulty.

On most of our controls, we have scans at several b-values, 1000, 3000, 5000, 
7000.

Is there a way to use all 4?

And even if there is, which would be the best single one to use?



Best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, February 14, 2018 6:22 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI



That's correct, you'd have to run TRACULA on a subject to get those files. 
They're computed from those 33 subjects, but you can't get the info without 
running it unfortunately.



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, February 14, 2018 5:19:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI



Thank you very much for getting back on this so promptly, a.y.



If I understand correctly, I think it's the information in the 
*_fsids_all_0_0_0.txt files from tracula runs on your training subjects, 
trc001-trc033, that would be best to use.



I see the trctrain directory with its contents in my Freesurfer 5.3 
installation and presume that this is all that's here. Are those .txt files 
readily available somewhere? Or do I need to do my own tracula runs to get them?



Or am I missing something?

I am a total newbie on tracula.



Best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, February 14, 2018 4:34 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI



Hi Donald - TRACULA doesn't use deterministic ROIs, instead it assigns a 
probability to any ROI to be the one t

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

[Krieger, Donald N.]

Dear a.y.

Thanks for getting back.
I've set the wheels in motion to run tracula on the control scans that we have.
I found your notes in the diffusion_tutorial download for grabbing the bval and 
bvecs from each DTI slice which looks like the biggest difficulty.
On most of our controls, we have scans at several b-values, 1000, 3000, 5000, 
7000.
Is there a way to use all 4?
And even if there is, which would be the best single one to use?

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, February 14, 2018 6:22 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI


That's correct, you'd have to run TRACULA on a subject to get those files. 
They're computed from those 33 subjects, but you can't get the info without 
running it unfortunately.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, February 14, 2018 5:19:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI


Thank you very much for getting back on this so promptly, a.y.



If I understand correctly, I think it's the information in the 
*_fsids_all_0_0_0.txt files from tracula runs on your training subjects, 
trc001-trc033, that would be best to use.



I see the trctrain directory with its contents in my Freesurfer 5.3 
installation and presume that this is all that's here. Are those .txt files 
readily available somewhere? Or do I need to do my own tracula runs to get them?



Or am I missing something?

I am a total newbie on tracula.



Best - Don



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, February 14, 2018 4:34 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI



Hi Donald - TRACULA doesn't use deterministic ROIs, instead it assigns a 
probability to any ROI to be the one that the specific tract intersects or 
neighbors at a specific position along that tract's trajectory. These prior 
probabilities are computed from the training subjects that make up the TRACULA 
atlas (where atlas here refers to a set of individuals rather than an average 
brain).



For what you're looking for, find the files: 
$yoursubject/dlabel/mni/*_fsids_all_0_0_0.txt



There is one file for each tract. The 0_0_0 in the file name means that you're 
looking at the ROIs that tract goes through (rather than the tract's left, 
right, etc neighbors - there are other files for those). In each of these 
files, each line corresponds to a different position along the tract. Since 
you're interested in the endpoints, you want to look at the first and the last 
line. The ID numbers in that file correspond to ROIs as specified in 
$FREESURFER_HOME/FreeSurferColorLUT.txt.



Hope this helps,

a.y



From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Krieger, Donald N." mailto:krieg...@upmc.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, February 14, 2018 at 10:19 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] List needed: pathway <==> freesurfer ROI



Dear List,



I need a list of Freesurfer ROIs which are typical endpoints for each standard 
pathway used in tracula.

I think this information is likely included in the default tracula atlas which 
I have been unable to find although I do not need spatial coordinates but 
rather just the list of ROI names for each pathway.

If this information is contained in publications, I would like to cite them.



I hope this is clear and thank you for any help you can provide.



Best - Don



Don Krieger, Ph.D.

Research Scientist

Department of Neurological Surgery

University of Pittsburgh


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Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

[Krieger, Donald N.]

Thank you very much for getting back on this so promptly, a.y.

If I understand correctly, I think it's the information in the 
*_fsids_all_0_0_0.txt files from tracula runs on your training subjects, 
trc001-trc033, that would be best to use.

I see the trctrain directory with its contents in my Freesurfer 5.3 
installation and presume that this is all that's here. Are those .txt files 
readily available somewhere? Or do I need to do my own tracula runs to get them?

Or am I missing something?
I am a total newbie on tracula.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Wednesday, February 14, 2018 4:34 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

Hi Donald - TRACULA doesn't use deterministic ROIs, instead it assigns a 
probability to any ROI to be the one that the specific tract intersects or 
neighbors at a specific position along that tract's trajectory. These prior 
probabilities are computed from the training subjects that make up the TRACULA 
atlas (where atlas here refers to a set of individuals rather than an average 
brain).

For what you're looking for, find the files: 
$yoursubject/dlabel/mni/*_fsids_all_0_0_0.txt

There is one file for each tract. The 0_0_0 in the file name means that you're 
looking at the ROIs that tract goes through (rather than the tract's left, 
right, etc neighbors - there are other files for those). In each of these 
files, each line corresponds to a different position along the tract. Since 
you're interested in the endpoints, you want to look at the first and the last 
line. The ID numbers in that file correspond to ROIs as specified in 
$FREESURFER_HOME/FreeSurferColorLUT.txt.

Hope this helps,
a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Krieger, Donald N." mailto:krieg...@upmc.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, February 14, 2018 at 10:19 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] List needed: pathway <==> freesurfer ROI

Dear List,

I need a list of Freesurfer ROIs which are typical endpoints for each standard 
pathway used in tracula.
I think this information is likely included in the default tracula atlas which 
I have been unable to find although I do not need spatial coordinates but 
rather just the list of ROI names for each pathway.
If this information is contained in publications, I would like to cite them.

I hope this is clear and thank you for any help you can provide.

Best - Don

Don Krieger, Ph.D.
Research Scientist
Department of Neurological Surgery
University of Pittsburgh

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[Freesurfer] List needed: pathway <==> freesurfer ROI

[Krieger, Donald N.]

Dear List,

I need a list of Freesurfer ROIs which are typical endpoints for each standard 
pathway used in tracula.
I think this information is likely included in the default tracula atlas which 
I have been unable to find although I do not need spatial coordinates but 
rather just the list of ROI names for each pathway.
If this information is contained in publications, I would like to cite them.

I hope this is clear and thank you for any help you can provide.

Best - Don

Don Krieger, Ph.D.
Research Scientist
Department of Neurological Surgery
University of Pittsburgh

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Re: [Freesurfer] recon-all error

[Krieger, Donald N.]

Hi Julia,

I’m sure one of the Freesurfer experts will reply soon.
Perhaps this will be helpful though.

It looks like recon-all is failing to find you dicom images.
You might want to post the recon-all command sequence you are using for them.

The first thing to check is that you are providing the name of one of the dicom 
files to recon-all, e.g.

recon-all -all -subject SubName -i full_pathname_of_one_of_the_dicom_files
recon-all -all -subject 173 -i 
/home/kriegerd/MriData/SubName/T1-Sagittal_MPRAGE_Iso_256x256.2/MR.1.3.12.2.1107.5.2.32.35217.2015051115153419213726461

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of "Julia Ströhlein"
Sent: Monday, January 22, 2018 9:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all error


Dear FreeSurfer developers,



I am new to FreeSurfer and this is the first time I am working with MR images.



I’ve been trying to run recon-all for my first subject and I keep getting 
errors like:



ERROR: GetDICOMInfo(): dcmGetDWIParams() 1

DICOM File: /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001

break DICOMRead.c:5228

Ref Series No = 9

Found 302 files, checking for dicoms

ERROR: don't know how to get DWI parameters from --Hitachi Medical Corporation 
--



The DICOM files are from an open 1,2 T MR Scanner from Hitachi Medical Systems. 
We used a T1 isoFSE sequence.



FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Platform: macOS High Sierra version 10.13.2



You will find the recon-all.log file attached.



Thank you very much,

Julia
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Re: [Freesurfer] Recon-all error: -autrecon2 unrecognized

[Krieger, Donald N.]

It looks like -autrecon2 is misspelled.
It should be -autorecon2

I hope this is helpful.

Best regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Gwang-Won Kim
Sent: Monday, May 22, 2017 7:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all error: -autrecon2 unrecognized

Hello FreeSurfer Developers,
I saw UserContributions/FAQ of FreeSurfer as following:
Q. I have already skull-stripped data. Can I submit it to recon-all?

A: If your skull-stripped volume does not have the cerebellum, then no. If it 
does, then yes, however you will have to run the data a bit differently.

First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s 

Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz 
and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this 
brainmask.mgz file and check that it looks okay (there is no skull, cerebellum 
is intact; use the sample subject bert that comes with your FreeSurfer 
installation to make sure it looks comparable). From there you can run the 
final stages of recon-all:
recon-all -autrecon2 -autorecon3 -s 



I tried to process recon-all -autrecon2 -autorecon3 -s .

But I have a problem.

Error message: Flag -autrecon2 unrecognized.



What is the problem?



1) FreeSurfer version: 6.0

2) Platform: CentOS release 6.8



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Re: [Freesurfer] Registration: Variable Must Begin with a Letter Error

[Krieger, Donald N.]

Whereever there are spaces in the pathname, add a "\" in front of the space and 
try again, e.g. instead of:


tkregisterfv --mov 
/Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET BRAIN 
TOF STATIC 2/2016004A/IM-0001-0001.dcm --reg 
/Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET BRAIN 
TOF STATIC 2/2016004A/IM-0001-0001.dcm --surfs



use:


tkregisterfv --mov 
/Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET\ 
BRAIN\ TOF\ STATIC 2/2016004A/IM-0001-0001.dcm --reg 
/Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET\ 
BRAIN\ TOF\ STATIC\ 2/2016004A/IM-0001-0001.dcm --surfs



I hope this is helpful - Don





> -Original Message-

> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-

> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve

> Sent: Wednesday, January 25, 2017 4:53 PM

> To: freesurfer@nmr.mgh.harvard.edu

> Subject: Re: [Freesurfer] Registration: Variable Must Begin with a Letter 
> Error

> 

>

> In the terminal output it says that your movable volume is

>

>

> /Users/djsandoval/Desktop/Selwyn/M87127996-

> 2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001-

> 0001.dcm

>

> not template.nii.gz. In principle, that should be fine, except that there are

> spaces in the path

>

> On 01/25/2017 04:34 PM, Anderson Napolitano wrote:

> >

> > Hello Experts!

> >

> >

> > I am having trouble checking the registration per step 2 of the pet

> > surfer tutorial: http://freesurfer.net/fswiki/PetSurfer. The line:

> > mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta

> > worked just fine but when checking the registration using the line:

> > tkregisterfv --mov template.nii.gz --reg template.reg.lta --surfs I

> > get the following output: set: Variable name must begin with a letter

> > As suggested by Dr. Greve, I've attached a text file documenting the

> > input, the output and the output with the debug flag on.

> > Please let me know if I can provide you any further details and I will

> > get to it as soon as I can.

> > Thank you very much for your time.

> > Warmest Regards,

> > Anderson

> >

> >

> >

> >

> >

> > ___

> > Freesurfer mailing list

> > Freesurfer@nmr.mgh.harvard.edu

> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

>

> /

> **

>Terminal Input

> 

> **/

>

> tkregisterfv --mov /Users/djsandoval/Desktop/Selwyn/M87127996-

> 2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001-

> 0001.dcm --reg /Users/djsandoval/Desktop/Selwyn/M87127996-

> 2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001-

> 0001.dcm --surfs

>

> /

> **

>Terminal Output

> 

> **/

>

> set: Variable name must begin with a letter

>

> /

> **

>Terminal Output with Debug Flag On

> 

> **/

>

> set echo = 1 ;

> breaksw

> breaksw

>

> end

> end

> while ( $#argv != 0 )

> while ( 5 != 0 )

>

> set flag = $argv[1] ; shift ;

> set flag = --mov

> shift

>

> switch ( $flag )

> switch ( --mov )

> if ( $#argv < 1 ) goto arg1err ;

> if ( 4 < 1 ) goto arg1err

> set movvol = $argv[1] ; shift ;

> set movvol =

> /Users/djsandoval/Desktop/Selwyn/M87127996-

> 2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001-

> 0001.dcm

> set: Variable name must begin with a letter.

> shift

>

> --

> Douglas N. Greve, Ph.D.

> MGH-NMR Center

> gr...@nmr.mgh.harvard.edu

> Phone Number: 617-724-2358

> Fax: 617-726-7422

>

> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

> www.nmr.mgh.harvard.edu/facility/filedrop/index.html

> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

>

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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 HelpLine

> at http://www.partners.org/complianceline . If the e

Re: [Freesurfer] Recon-all: stochastic mri_nu_correct error when run on HPC cluster

[Krieger, Donald N.]

Pardon me for poking in here.  I hope this is helpful.
It looks like the failure is on an lseek command which means the file isn't 
there or was truncated, as Zeke suggests.
When you deploy your jobs to the cloud cluster, perhaps there's a directive 
which can be tweaked to give you a bigger playpen.

Best - Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
> Sent: Friday, November 18, 2016 10:36 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Recon-all: stochastic mri_nu_correct error when run 
> on
> HPC cluster
> 
> That is a very odd error and I havent seen anything like it that I can recall.
> 
> My initial thoughts are that the nu_evaluate and nu_correct commands are part
> of the mni tools shipped with freesurfer. The mni tools do a lot of reading,
> writing and deleting of temporary files. (You can see how it mentions
> 'tmp.mri_nu_correct.mni.223851' in the log file you sent).
> 
> It's possible that your cluster has limits on the I/O (our does and the mni 
> tools
> were the culprit on our case). Maybe its deleting some of these temp files or
> perhaps the temporary space is just getting filled.
> This could cause the nu_evaluate command to fail in an ungraceful way.
> 
> 
> 
> On 11/17/2016 05:14 PM, Anders Perrone wrote:
> > Hi FreeSurfer Developers,
> >
> >
> >
> > I'm running freesurfer from the HCP pipeline developed by the
> > Washington University in St. Louis. It ran just fine on our
> > university's cluster, but when I migrated the pipeline to Exacloud,
> > Intel's HPC cluster, the recon-all command began randomly failing.
> > Occasionally it will work on the first try, but more often than not
> > the same command has to be re-run upwards of 30 times before it will
> > succeed. I've provided the recon-all command and the relevant section
> > of the log file including the error here (attached is the full 
> > recon-all.log file):
> >
> >
> >
> > recon-all -i ./T1w/T1w_acpc_dc_restore_1mm.nii.gz -subjid ${SUBJECT_ID}
> > -sd . /T1w -motioncor -talairach -nuintensitycor -normalization
> >
> >
> >
> > ...
> >
> > [perronea@exanode-3-9.local${PWD}/T1w/washu_INV0WC5U4JA/mri/]
> > [2016-11-17 13:08:38] running:
> >
> >
> > /home/exacloud/lustre1/users/mirandad/usr/local/freesurfer53/mni/bin/m
> > ake_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.223851/nu1.mnc
> > ./tmp.mri_nu_correct.mni.223851/1//template.mnc
> >
> >
> >
> > Transforming
> > slices:...
> > ...Done
> >
> > Transforming
> >
> slices:...
> ..mincresample:
> > posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp ==
> > lseek(nciop->fd, 0, 1)' failed.
> >
> > nu_evaluate: crashed while running mincresample (termination
> > status=134)
> >
> > nu_correct: crashed while running nu_evaluate (termination
> > status=65280)
> >
> > ERROR: nu_correct
> >
> > Linux exanode-3-9.local 2.6.32-504.30.3.el6.x86_64 #1 SMP Wed Jul 15
> > 10:13:09 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> >
> >
> >
> > recon-all -s washu_INV0WC5U4JA exited with ERRORS at Thu Nov 17
> > 13:08:40 PST 2016
> >
> >
> >
> > It doesn't appear than any similar errors have been reported on
> > freesurfer. Our current work-around is to simply re-run the job on
> > different nodes until it works, but this is not a sustainable
> > long-term solution. Any guidance on troubleshooting this error would
> > be greatly appreciated.
> >
> >
> >
> > FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> >
> > Platform: CentOS release 6.5 (FINAL)
> >
> > uname -a: Linux exalab3.ohsu.edu 2.6.32-504.12.2.el6.x86_64 #1 SMP Wed
> > Mar 11 22:03:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
> >
> >
> >
> > Thanks,
> >
> > Anders
> >
> >
> >
> >
> >
> > Anders Perrone,
> >
> > Research Assistant I
> >
> > Fair Neuroimaging Lab
> >
> >
> >
> > perro...@ohsu.edu 
> >
> > 503-418-1897
> >
> >
> >
> > Oregon Health & Science University
> >
> > Mail code:L470
> >
> > 3181 SW Sam Jackson Park Road
> >
> > Portland, Oregon 97239-3098
> >
> >
> >
> >
> >
> > "If there is no solution to the problem then don't waste time worrying
> > about it. If there is a solution to the problem then don't waste time
> > worrying about it." - Dalai Lama XIV
> >
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is

Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

[Krieger, Donald N.]

Now I don't understand.

Here's the situation:
Someone has given me a bunch of MEG's with freesurfer runs which were run using 
both a T1 and a T2 scan with -T2pial .
 Mri_info --tkr2scanner gives the same transform for aparac+aseg.mgz, T1.mgz, 
and T2.mgz  .
I will be coregistering the MEG which comes with each T1/T2 pair .
Since I'm getting the same transform from all the .mgz's, I speculated that 
freesurfer transformed both scans to tkr coordinates, did its thing, and then 
picked the T1 to provide the tkr2scanner transform.  
???

Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Friday, November 11, 2016 4:35 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple 
> input
> scans
> 
> If the head has not moved, then they will share a scanner RAS, ie,  a given
> scanner RAS will be at the same place in the head in the two scans, though 
> they
> will map to different col,row,slice in their respective volumes. If the head 
> has
> moved, then you will need to perform a registration to get them aligned.
> 
> 
> On 11/11/2016 04:17 PM, Krieger, Donald N. wrote:
> > Thanks for getting back, Doug.
> > I understand - but if there are two scans, aren't there two scanner RAS's 
> > since
> the head presumably moved at least a little from one to the other or the scans
> could have been done on different scanners?
> >
> > Don
> >
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> > [gr...@nmr.mgh.harvard.edu]
> > Sent: Friday, November 11, 2016 3:22 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with
> > multiple input scans
> >
> > -tkr2scanner gives the transform that takes "tkregister RAS" and
> > converts it to scanner RAS. "tkregisterRAS" is the RAS system used by
> > surfaces (it, a vertex xyz is in tkregisterRAS). See
> > http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> >
> >
> >
> > On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
> >> If I run recon-all with both a T1 and a T2 scan and switch t2pial,
> >> does mri_info -tkr2scanner give me the transform to the T1 scanner
> >> frame of reference?
> >>
> >> And if I run recon-all with many T1's , what does mri_info
> >> -tkr2scanner give me then?
> >>
> >> Thanks - Don
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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
> > . 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.
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> 
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
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Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

[Krieger, Donald N.]

Thanks for getting back, Doug.
I understand - but if there are two scans, aren't there two scanner RAS's since 
the head presumably moved at least a little from one to the other or the scans 
could have been done on different scanners?

Don


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, November 11, 2016 3:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple 
input scans

-tkr2scanner gives the transform that takes "tkregister RAS" and
converts it to scanner RAS. "tkregisterRAS" is the RAS system used by
surfaces (it, a vertex xyz is in tkregisterRAS). See
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems



On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
>
> If I run recon-all with both a T1 and a T2 scan and switch t2pial,
> does mri_info –tkr2scanner give me the transform to the T1 scanner
> frame of reference?
>
> And if I run recon-all with many T1’s , what does mri_info
> –tkr2scanner give me then?
>
> Thanks - Don
>
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

[Krieger, Donald N.]

If I run recon-all with both a T1 and a T2 scan and switch t2pial, does 
mri_info -tkr2scanner give me the transform to the T1 scanner frame of 
reference?

And if I run recon-all with many T1's , what does mri_info -tkr2scanner give me 
then?

Thanks - Don

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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Krieger, Donald N.]

Thank you - very helpful.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Tuesday, August 30, 2016 10:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run


ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out

On 8/30/16 10:12 AM, Krieger, Donald N. wrote:
Dear list:

What are the advantages of including a T2 scan when running recon-all -all  ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/

Thanks and best - Don





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[Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Krieger, Donald N.]

Dear list:

What are the advantages of including a T2 scan when running recon-all -all  ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/

Thanks and best - Don

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Re: [Freesurfer] question about exporting volumes

[Krieger, Donald N.]

Hi Dorsa,

ImageJ and the people on the ImageJ mailing list may be helpful in transforming 
one of the standard output formats provided by freeview, e.g. nii, to a 
standard input format provided by COMSOL.
Here's a useful link.
  http://imagej.nih.gov/ij/list.html 

HTH - Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, July 07, 2016 12:29 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] question about exporting volumes
> 
> You can view it in freesurfer with
> cd $SUBJECTS_DIR/subject/mri
> freeview -v orig.mgz -v
> aseg.mgz:lut=$FREESURFER_HOME/FreeSurferColorLUT.txt:opacity=.3:colormap
> =lut
> 
> I don't know anything about COMSOL
> 
> 
> On 07/07/2016 12:25 PM, Dorsa Haji Ghaffari wrote:
> > Thank you. I want to view the thalamus as a volume in freesurfer. Do
> > you know how to do that? also by exporting I mean exporting it as a
> > volume and then import it into COMSOL as a geometry.
> >
> > Thank you for your help!
> >
> > Dorsa
> >
> >
> > On Wed, Jul 6, 2016 at 7:50 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > what do you mean isolate? what do you mean export? You can create a
> > binary mask in nifti format with mri_binarize --i aseg.mgz --match
> > 10 49
> > --o thalamus.mask.nii.gz
> >
> >
> > On 07/06/2016 04:46 PM, Dorsa Haji Ghaffari wrote:
> > >
> > >
> > >
> > > Hi,
> > >
> > > I was able to segment the MRI successfully, now I am trying to
> > isolate
> > > the thalamus and export it out of FS as a volume. Is there a way
> > to do
> > > that in FS?
> > >
> > > Thank you
> > >
> > > Dorsa
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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 . 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@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
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Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

[Krieger, Donald N.]

Hi Renata,

Is there a problem with the “-s” argument, i.e. the “/” in  - s 20110815/

HTH - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Vaz pandolfo, 
Renata
Sent: Thursday, July 07, 2016 8:05 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

Dear FreeSurfer developers,
I am running recon-all on a healthy subject and I am also trying to get the 
hippocampal subfields segmentation.
On the mri directory there is no hippocampus output, and the recon-all exited 
with errors.
From my understanding, the error is with the lh.BA1_exvivo.label:

SUBJECTS_DIR
/home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Invalid argument
ERROR reading 
/home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label

The command I used was:
recon-all -all \
-i 
~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz
 -s 20110815/ \
-sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
-T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \
-T2pial -hippocampal-subfields-T1


When trying to solve the problem, I noticed that I could have run a separate 
command for the hippocampal subfields and I ran this one:

recon-all \
-s 20110815/ \
-sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
-hippocampal-subfields-T1T2 
~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
  20110815_T2
Since the previous data had errors, I didn't really expect this to work, but I 
tried it anyways.
It exited "without errors", but on the log there was the following error twice:

Error:Cannot find CTF archive 
/usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf
Extra info:
Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611
uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 
2016 x86_64 x86_64 x86_64 GNU/Linux
logs: recon-all and hippocampal-subfields-T1T2 attached
If anyone has had the same problem, could you please tell me how to solve it?
And if I am doing something wrong, please tell me the correct way so I can 
continue with the analysis.

Thank you!
Renata
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[Freesurfer] dynamic monitor: freesurfer jobs on the Open Science Grid

[Krieger, Donald N.]

For those who are interested, we have deployed a crude dynamic monitor for 
freesurfer jobs running on the Open Science Grid.
It can be viewed at 
http://xd-login.opensciencegrid.org/scratch/donkri/fsurfPoll.html .
The display information is in addition to that which is currently accessible 
via "fsurf list" .

Each job runs in a sequence of three steps.
The second step runs in parallel as two separate OSG jobs.
These are your "recon-all -autorecon2" jobs.
At the lower right corner of the webpage, the number of jobs for each user at 
each step is listed.

Best - Don

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[Freesurfer] Announcement: fsurf, a command line tool for running freesurfer on the Open Science Grid

[Krieger, Donald N.]

Dear FreeSurfer community,

The Open Science Grid (http://www.opensciencegrid.org) is a federation of 
university and laboratory HPC facilities which share computing capacity to 
support science.
We have developed a command line tool "fsurf" you can use from your laptop or 
desktop computer to submit scans for FreeSurfer processing on these clusters.
In the initial release it is capable of executing "recon-all -all -i 
SubjectName.mgz" using FreeSurfer 5.3.

No allocation is required.
We only request that you cite the OSG in publications that benefit from its use.
Instructions for getting started are found here: 
http://bit.ly/freesurferopensciencegrid.

Please post questions and problems to OSG user support at 
user-supp...@opensciencegrid.org.
We hope you find it useful.

Best regards,

The OSG fsurf support team

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Re: [Freesurfer] tutorial_data

[Krieger, Donald N.]

I can see the sub directories and the distributions via ftp.

Best - Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, June 29, 2016 10:57 AM
> To: Freesurfer support list
> Cc: bruno fraccini pastorello
> Subject: Re: [Freesurfer] tutorial_data
> 
> try again - hopefully the stale mounts of been fixed now cheers Bruce
> 
> 
> On Wed, 29 Jun 2016, Bennet Fauber wrote:
> 
> > Looks like all downloads are broken, as the same message appears when
> > trying to download the binary distribution,
> >
> > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-
> > Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
> >
> > There are no files on the server advertised to the public:
> >
> > Name (surfer.nmr.mgh.harvard.edu:bennet): anonymous
> > 331 Please specify the password.
> > Password:
> > 230 Login successful.
> > Remote system type is UNIX.
> > Using binary mode to transfer files.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,246).
> > 150 Here comes the directory listing.
> > -rw-r-1 048286 Jul 03  2013 index.html
> > drwxr-xr-x2 004096 Jul 24  2015 pub
> > drwxr-xr-x2 004096 Nov 20  2012 transfer
> > 226 Directory send OK.
> > ftp> cd pub
> > 250 Directory successfully changed.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,224).
> > 150 Here comes the directory listing.
> > 226 Directory send OK.
> > ftp> cd ../transfer
> > 250 Directory successfully changed.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,237).
> > 150 Here comes the directory listing.
> > 226 Directory send OK.
> >
> >
> >
> >
> > On Tue, Jun 28, 2016 at 1:32 PM, bruno fraccini pastorello
> >  wrote:
> >> Dear freesurfer support,
> >> I'm trying to download the freesurfer data to learn freesurfer, but i
> >> can't it. Do you know why? Could you help me?
> >>
> >> I tried use this link
> >> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and I
> >> obtain this error: Safari cant open the page
> >> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz
> >> because Safari can't load any data from this location.
> >>
> >> Thanks in advance
> >> Bruno Pastorello
> >>
> >> PS: I tried use this link too
> >> :https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data  using
> >> curl command on terminal and it has failed too
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> 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 . 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.
> >>
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
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Re: [Freesurfer] tutorial_data

[Krieger, Donald N.]

It looks like things aren't quite linked up.
I can reach the server with ftp and I can see directory pub.
But there's no directory pub/dist  .

Best - Don

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, June 29, 2016 10:13 AM
> To: Freesurfer support list
> Cc: bruno fraccini pastorello
> Subject: Re: [Freesurfer] tutorial_data
> 
> it should all be working now, no?
> On Wed, 29 Jun 2016, Bennet Fauber wrote:
> 
> > Looks like all downloads are broken, as the same message appears when
> > trying to download the binary distribution,
> >
> > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-
> > Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
> >
> > There are no files on the server advertised to the public:
> >
> > Name (surfer.nmr.mgh.harvard.edu:bennet): anonymous
> > 331 Please specify the password.
> > Password:
> > 230 Login successful.
> > Remote system type is UNIX.
> > Using binary mode to transfer files.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,246).
> > 150 Here comes the directory listing.
> > -rw-r-1 048286 Jul 03  2013 index.html
> > drwxr-xr-x2 004096 Jul 24  2015 pub
> > drwxr-xr-x2 004096 Nov 20  2012 transfer
> > 226 Directory send OK.
> > ftp> cd pub
> > 250 Directory successfully changed.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,224).
> > 150 Here comes the directory listing.
> > 226 Directory send OK.
> > ftp> cd ../transfer
> > 250 Directory successfully changed.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,237).
> > 150 Here comes the directory listing.
> > 226 Directory send OK.
> >
> >
> >
> >
> > On Tue, Jun 28, 2016 at 1:32 PM, bruno fraccini pastorello
> >  wrote:
> >> Dear freesurfer support,
> >> I'm trying to download the freesurfer data to learn freesurfer, but i
> >> can't it. Do you know why? Could you help me?
> >>
> >> I tried use this link
> >> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and I
> >> obtain this error: Safari cant open the page
> >> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz
> >> because Safari can't load any data from this location.
> >>
> >> Thanks in advance
> >> Bruno Pastorello
> >>
> >> PS: I tried use this link too
> >> :https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data  using
> >> curl command on terminal and it has failed too
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> 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 . 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.
> >>
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
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Re: [Freesurfer] "wm" boundaries and stats

[Krieger, Donald N.]

Thanks very much, Doug.
I could always hope.

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, March 03, 2016 12:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] "wm" boundaries and stats
> 
> Hi Don, there is not an easy way to get this information. You can use
> mri_binarize to create a surface of each ROI, something like
> 
> mri_binarize --i wmparc.mgz --match 3013 --surf lh.wm.lingual
> 
> Use this version of mri_binarize
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
> 
> but doing the other things you want is a real programming job
> 
> doug
> 
> 
> On 03/01/2016 09:29 AM, Krieger, Donald N. wrote:
> >
> > Freesurfer provides 34 ctx label volumes on each side of the brain
> > with adjacent wm labels.
> >
> > The boundary between each ctx volume and the co-named adjacent wm
> > volume is a third "white" label.
> >
> > I would like to extract a few pieces of information from the analogous
> > boundary between each wm volume and those adjacent volumes to it which
> > are not the co-named ctx volume.
> >
> > For instance many wm volumes share a boundary with the unsegmented
> > white matter.
> >
> > Some share a boundary with sub-cortical structures.
> >
> > Here are some of the information I would like to extract.
> >
> > What do you think?
> >
> > What are the xyz coordinates of the complete boundary surrounding each
> > wm volume and what is the name of the adjacent volume for each point
> > on the boundary?
> >
> > I understand that for the boundary between the ctx volume and the
> > adjacent wm volume, the white label provides this information.
> >
> > What is the percentage and area of the complete boundary surrounding a
> > wm volume which is adjacent to the co-named ctx volume.?
> >
> > What are the names of the other volumes with which each wm volume
> > shares a boundary and what is the percentage and area of the boundary
> > shared with each?
> >
> > For each point within a wm volume, are the nearest points on the wm
> > boundary adjacent to the co-named ctx volume or are some adjacent to
> > unsegmented white matter or sub-cortical structures?
> >
> > More generally, is a particular few mm voxel surrounded by gray matter
> > and so is likely primarily composed primarily of relatively short
> > range fibers or is it adjacent to the deep white matter (unsegmented)
> > and likely composed of a mix of relatively short range fibers and long
> > range "en passage" fibers.
> >
> > It is this last question which most closely gets at the ideas I wish
> > to explore.
> >
> > We are able to measure electric current in the white matter with mm
> > resolution from the MEG.
> >
> > The mix of local and "en passage" fibers should effect the direction
> > of the electric currents in the white matter and I can measure that.
> >
> > The distance scale is at the edge of that provided by DTI-derived
> > tractography so we may be able to meld these measurements with those.
> >
> > Your thoughts would be welcome on what is already there in freesurfer
> > that will help with this and what you think might be a good direction
> > to proceed to develop what we need from what is there.
> >
> > Thanks - Don
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 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 . 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] "wm" boundaries and stats

[Krieger, Donald N.]

Freesurfer provides 34 ctx label volumes on each side of the brain with 
adjacent wm labels.
The boundary between each ctx volume and the co-named adjacent wm volume is a 
third "white" label.
I would like to extract a few pieces of information from the analogous boundary 
between each wm volume and those adjacent volumes to it which are not the 
co-named ctx volume.
For instance many wm volumes share a boundary with the unsegmented white matter.
Some share a boundary with sub-cortical structures.

Here are some of the information I would like to extract.
What do you think?

What are the xyz coordinates of the complete boundary surrounding each wm 
volume and what is the name of the adjacent volume for each point on the 
boundary?
I understand that for the boundary between the ctx volume and the adjacent wm 
volume, the white label provides this information.

What is the percentage and area of the complete boundary surrounding a wm 
volume which is adjacent to the co-named ctx volume.?

What are the names of the other volumes with which each wm volume shares a 
boundary and what is the percentage and area of the boundary shared with each?

For each point within a wm volume, are the nearest points on the wm boundary 
adjacent to the co-named ctx volume or are some adjacent to unsegmented white 
matter or sub-cortical structures?
More generally, is a particular few mm voxel surrounded by gray matter and so 
is likely primarily composed primarily of relatively short range fibers or is 
it adjacent to the deep white matter (unsegmented) and likely composed of a mix 
of relatively short range fibers and long range "en passage" fibers.
It is this last question which most closely gets at the ideas I wish to explore.
We are able to measure electric current in the white matter with mm resolution 
from the MEG.
The mix of local and "en passage" fibers should effect the direction of the 
electric currents in the white matter and I can measure that.
The distance scale is at the edge of that provided by DTI-derived tractography 
so we may be able to meld these measurements with those.

Your thoughts would be welcome on what is already there in freesurfer that will 
help with this and what you think might be a good direction to proceed to 
develop what we need from what is there.

Thanks - Don

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[Freesurfer] repost: more on comparing runs on the same scan

[Krieger, Donald N.]

Hi everyone,

I'm reposting this from 2 days ago.
Please excuse if someone responded and I missed it.

We have been able to establish that we are getting identical results when 
running recon-all -all on the same scan on different machine for the following:
All .mgz files in directories mri, mri/orig, and mri/transforms, by comparing 
using mri_diff ...
All of the .label and .annot files in directory label with md5sum ...
Many of the files in directory surf with mris_diff.

We continue to see differences in the label/BA*.annot files and in about 20 of 
the files in surf including [lr]h.inflated|orig|pial .
We do see identity for lh.area.pial but not for lh.pial for instance.
I've attached the output of our test routine.

Your thoughts would be welcome on this pesky question.

Best - Don

MRN_1_comet_diamond =?= MRN_1_mwt2_2_diamond ...
... directory mri ...
aparc.a2009s+aseg.mgz ok
aparc+aseg.mgz ok
aseg.auto.mgz ok
aseg.auto_noCCseg.mgz ok
aseg.mgz ok
brain.finalsurfs.mgz ok
brainmask.auto.mgz ok
brainmask.mgz ok
brain.mgz ok
ctrl_pts.mgz ok
filled.mgz ok
lh.ribbon.mgz ok
norm.mgz ok
nu.mgz ok
nu_noneck.mgz ok
orig.mgz ok
orig_nu.mgz ok
rawavg.mgz ok
rh.ribbon.mgz ok
ribbon.mgz ok
T1.mgz ok
wm.asegedit.mgz ok
wm.mgz ok
wmparc.mgz ok
wm.seg.mgz ok
... directory mri/orig ...
001.mgz ok
... directory mri/transforms ...
talairach.m3z.inv.x.mgz ok
talairach.m3z.inv.y.mgz ok
talairach.m3z.inv.z.mgz ok
... directory surf ...
lh.area ok
lh.area.mid ok
lh.area.pial ok
lh.avg_curv ok
lh.curv ok
lh.curv.pial ok
lh.defect_borders ok
lh.defect_chull ok
lh.defect_labels ok
lh.inflated Surfaces are not the same
lh.inflated.H ok
lh.inflated.K ok
lh.inflated.nofix Surfaces are not the same
lh.jacobian_white ok
lh.orig Surfaces are not the same
lh.orig.nofix Surfaces are not the same
lh.pial Surfaces are not the same
lh.qsphere.nofix Surfaces are not the same
lh.smoothwm Surfaces are not the same
lh.smoothwm.BE.crv ok
lh.smoothwm.C.crv ok
lh.smoothwm.FI.crv ok
lh.smoothwm.H.crv ok
lh.smoothwm.K1.crv ok
lh.smoothwm.K2.crv ok
lh.smoothwm.K.crv ok
lh.smoothwm.nofix Surfaces are not the same
lh.smoothwm.S.crv ok
lh.sphere Surfaces are not the same
lh.sphere.reg Surfaces are not the same
lh.sulc ok
lh.thickness ok
lh.volume ok
lh.w-g.pct.mgh ok
lh.white Surfaces are not the same
rh.area ok
rh.area.mid ok
rh.area.pial ok
rh.avg_curv ok
rh.curv ok
rh.curv.pial ok
rh.defect_borders ok
rh.defect_chull ok
rh.defect_labels ok
rh.inflated Surfaces are not the same
rh.inflated.H ok
rh.inflated.K ok
rh.inflated.nofix Surfaces are not the same
rh.jacobian_white ok
rh.orig Surfaces are not the same
rh.orig.nofix Surfaces are not the same
rh.pial Surfaces are not the same
rh.qsphere.nofix Surfaces are not the same
rh.smoothwm Surfaces are not the same
rh.smoothwm.BE.crv ok
rh.smoothwm.C.crv ok
rh.smoothwm.FI.crv ok
rh.smoothwm.H.crv ok
rh.smoothwm.K1.crv ok
rh.smoothwm.K2.crv ok
rh.smoothwm.K.crv ok
rh.smoothwm.nofix Surfaces are not the same
rh.smoothwm.S.crv ok
rh.sphere Surfaces are not the same
rh.sphere.reg Surfaces are not the same
rh.sulc ok
rh.thickness ok
rh.volume ok
rh.w-g.pct.mgh ok
rh.white Surfaces are not the same
label files ok
... directory label/*.annot ...
lh.aparc.a2009s.annot ok
lh.aparc.annot ok
lh.aparc.DKTatlas40.annot ok
lh.BA.annot not ok ... 29d66ea8614488a56cb74e5cc5fe9470 != 
bc9507b6e0c7051b7e89554beb5d875f
lh.BA.thresh.annot not ok ... 3b51e59d298014da180ee266d29805b8 != 
576a09cfa118ed245b4103ca7f5f6753
rh.aparc.a2009s.annot ok
rh.aparc.annot ok
rh.aparc.DKTatlas40.annot ok
rh.BA.annot not ok ... 7b1b4e8ea47f9fa366d8bff5079fe0c1 != 
a062a4b0494d64ac958894621161499d
rh.BA.thresh.annot not ok ... af3a74b7f59a9924857d65678ca57fde != 
7de02e148e7000f51ca9ef0d7816e834
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[Freesurfer] more on comparing runs on the same scan

[Krieger, Donald N.]

We have been able to establish that we are getting identical results when 
running recon-all -all on the same scan on different machine for the following:
All .mgz files in directories mri, mri/orig, and mri/transforms, by comparing 
using mri_diff ...
All of the .label and .annot files in directory label with md5sum ...
Many of the files in directory surf with mris_diff.

We see differences in the BA*.annot files.
We are still seeing difference in about 20 of the files in surf including 
[lr]h.inflated|orig|pial .
We do see identity for lh.area.pial but not for lh.pial for instance.
I've attached the output of our test routine.

Your thoughts would be welcome on this pesky question.

Best - Don

MRN_1_comet_diamond =?= MRN_1_mwt2_2_diamond ...
... directory mri ...
aparc.a2009s+aseg.mgz ok
aparc+aseg.mgz ok
aseg.auto.mgz ok
aseg.auto_noCCseg.mgz ok
aseg.mgz ok
brain.finalsurfs.mgz ok
brainmask.auto.mgz ok
brainmask.mgz ok
brain.mgz ok
ctrl_pts.mgz ok
filled.mgz ok
lh.ribbon.mgz ok
norm.mgz ok
nu.mgz ok
nu_noneck.mgz ok
orig.mgz ok
orig_nu.mgz ok
rawavg.mgz ok
rh.ribbon.mgz ok
ribbon.mgz ok
T1.mgz ok
wm.asegedit.mgz ok
wm.mgz ok
wmparc.mgz ok
wm.seg.mgz ok
... directory mri/orig ...
001.mgz ok
... directory mri/transforms ...
talairach.m3z.inv.x.mgz ok
talairach.m3z.inv.y.mgz ok
talairach.m3z.inv.z.mgz ok
... directory surf ...
lh.area ok
lh.area.mid ok
lh.area.pial ok
lh.avg_curv ok
lh.curv ok
lh.curv.pial ok
lh.defect_borders ok
lh.defect_chull ok
lh.defect_labels ok
lh.inflated Surfaces are not the same
lh.inflated.H ok
lh.inflated.K ok
lh.inflated.nofix Surfaces are not the same
lh.jacobian_white ok
lh.orig Surfaces are not the same
lh.orig.nofix Surfaces are not the same
lh.pial Surfaces are not the same
lh.qsphere.nofix Surfaces are not the same
lh.smoothwm Surfaces are not the same
lh.smoothwm.BE.crv ok
lh.smoothwm.C.crv ok
lh.smoothwm.FI.crv ok
lh.smoothwm.H.crv ok
lh.smoothwm.K1.crv ok
lh.smoothwm.K2.crv ok
lh.smoothwm.K.crv ok
lh.smoothwm.nofix Surfaces are not the same
lh.smoothwm.S.crv ok
lh.sphere Surfaces are not the same
lh.sphere.reg Surfaces are not the same
lh.sulc ok
lh.thickness ok
lh.volume ok
lh.w-g.pct.mgh ok
lh.white Surfaces are not the same
rh.area ok
rh.area.mid ok
rh.area.pial ok
rh.avg_curv ok
rh.curv ok
rh.curv.pial ok
rh.defect_borders ok
rh.defect_chull ok
rh.defect_labels ok
rh.inflated Surfaces are not the same
rh.inflated.H ok
rh.inflated.K ok
rh.inflated.nofix Surfaces are not the same
rh.jacobian_white ok
rh.orig Surfaces are not the same
rh.orig.nofix Surfaces are not the same
rh.pial Surfaces are not the same
rh.qsphere.nofix Surfaces are not the same
rh.smoothwm Surfaces are not the same
rh.smoothwm.BE.crv ok
rh.smoothwm.C.crv ok
rh.smoothwm.FI.crv ok
rh.smoothwm.H.crv ok
rh.smoothwm.K1.crv ok
rh.smoothwm.K2.crv ok
rh.smoothwm.K.crv ok
rh.smoothwm.nofix Surfaces are not the same
rh.smoothwm.S.crv ok
rh.sphere Surfaces are not the same
rh.sphere.reg Surfaces are not the same
rh.sulc ok
rh.thickness ok
rh.volume ok
rh.w-g.pct.mgh ok
rh.white Surfaces are not the same
label files ok
... directory label/*.annot ...
lh.aparc.a2009s.annot ok
lh.aparc.annot ok
lh.aparc.DKTatlas40.annot ok
lh.BA.annot not ok ... 29d66ea8614488a56cb74e5cc5fe9470 != 
bc9507b6e0c7051b7e89554beb5d875f
lh.BA.thresh.annot not ok ... 3b51e59d298014da180ee266d29805b8 != 
576a09cfa118ed245b4103ca7f5f6753
rh.aparc.a2009s.annot ok
rh.aparc.annot ok
rh.aparc.DKTatlas40.annot ok
rh.BA.annot not ok ... 7b1b4e8ea47f9fa366d8bff5079fe0c1 != 
a062a4b0494d64ac958894621161499d
rh.BA.thresh.annot not ok ... af3a74b7f59a9924857d65678ca57fde != 
7de02e148e7000f51ca9ef0d7816e834
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Re: [Freesurfer] Freesurfer tool to automatically generate label surrounding a given vertex?

[Krieger, Donald N.]

Yes, thanks ... from my notes:
This command contracts the selected surface vectors 3.0 mm and 
places the resultant new surface file in surf/lh.white-3:
mris_expand lh.white -3.0 lh.white-3

Best regards,
 
Don
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Saturday, February 13, 2016 2:37 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Freesurfer tool to automatically generate label
> surrounding a given vertex?
> 
> mris_expand probably
> On Sat, 13 Feb 2016, Krieger, Donald N. wrote:
> 
> > Thanks for posting back about this, Bruce.
> > I am thinking about a different function which probably is not called 
> > --dilate.
> > One specifies a surface, e.g. white, and gets back a new surface displaced 
> > by
> the distance you specify whose tangent is parallel to the tangent of the 
> starting
> surface at the nearest point.
> >
> >
> >> -Original Message-
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> >> Sent: Saturday, February 13, 2016 1:44 PM
> >> To: Freesurfer support list
> >> Subject: Re: [Freesurfer] Freesurfer tool to automatically generate
> >> label surrounding a given vertex?
> >>
> >> Hi Don
> >>
> >> I think label2label --dilate does a morphological dilation on the
> >> surface, not a new surface. It is also independent of distance - it
> >> just uses topology - so your approach will be better if you truly
> >> want a circle (although of course if the surface is highly curved
> >> then the metric won't be quite right)
> >>
> >> cheers
> >> Bruce
> >> On Sat, 13 Feb 2016, Krieger, Donald N. wrote:
> >>
> >>>
> >>> Hi Martha,
> >>>
> >>>
> >>>
> >>> A brute force but simple way to do this is to use the list of labels
> >>> contained in subjects/nnn/label/lh.cortex and rh.cortex.
> >>>
> >>> Given a vertex x,y,z, go through the file and select the lines for
> >>> which the distance to x,y,z <= 2 mm.  This will give you a bunch of
> >>> labels for points within a circle with 2 mm radius about x,y,z.  And
> >>> all of them will be on the “white” surface.  If your vertex is on a
> >>> different surface, e.g. pia, or you want a different geometry, e.g.
> >>> square, there’s likely a simple variant which will work.
> >>>
> >>>
> >>>
> >>> In my experience mri_label2label –dilate takes a lot of time and I’m
> >>> not sure you can restrict it to give you points on the surface that
> >>> you want.  I think it gives you a new surface which is displaced by
> >>> a fixed distance from the one where you start.
> >>>
> >>>
> >>>
> >>> I hope this is helpful.
> >>>
> >>>
> >>>
> >>> Best - Don
> >>>
> >>>
> >>>
> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu
> >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martha
> >>> Shiell
> >>> Sent: Saturday, February 13, 2016 12:59 PM
> >>> To: freesurfer@nmr.mgh.harvard.edu
> >>> Subject: [Freesurfer] Freesurfer tool to automatically generate
> >>> label surrounding a given vertex?
> >>>
> >>>
> >>>
> >>> Hello Freesurfer community,
> >>>
> >>>
> >>>
> >>> I am looking for a way to automatically generate a surface label
> >>> file of a specific dimension (e.g. a circle with a specific
> >>> diameter, or a square), given a specific vertex and some measure of the
> desired size.
> >>>
> >>>
> >>>
> >>> I have considered to do so by starting with a label file consisting
> >>> of a single vertex, and then expanding this label with the
> >>> mri_label2label tool, using the --dilate option. I wanted to know
> >>> though if anyone has any better suggestions.
> >>>
> >>>
> >>>
> >>> Thank you,
> >>>
> >>> Martha
> >>>
> >>>
> >>>
> >>> --
> >>>
> >>> Martha M. Shiell, PhD
> >>>
> >>>
> >>>
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >

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Re: [Freesurfer] Freesurfer tool to automatically generate label surrounding a given vertex?

[Krieger, Donald N.]

Thanks for posting back about this, Bruce.
I am thinking about a different function which probably is not called --dilate.
One specifies a surface, e.g. white, and gets back a new surface displaced by 
the distance you specify whose tangent is parallel to the tangent of the 
starting surface at the nearest point.


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Saturday, February 13, 2016 1:44 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Freesurfer tool to automatically generate label
> surrounding a given vertex?
> 
> Hi Don
> 
> I think label2label --dilate does a morphological dilation on the surface, 
> not a
> new surface. It is also independent of distance - it just uses topology - so 
> your
> approach will be better if you truly want a circle (although of course if the
> surface is highly curved then the metric won't be quite right)
> 
> cheers
> Bruce
> On Sat, 13 Feb 2016, Krieger, Donald N. wrote:
> 
> >
> > Hi Martha,
> >
> >
> >
> > A brute force but simple way to do this is to use the list of labels
> > contained in subjects/nnn/label/lh.cortex and rh.cortex.
> >
> > Given a vertex x,y,z, go through the file and select the lines for
> > which the distance to x,y,z <= 2 mm.  This will give you a bunch of
> > labels for points within a circle with 2 mm radius about x,y,z.  And
> > all of them will be on the “white” surface.  If your vertex is on a
> > different surface, e.g. pia, or you want a different geometry, e.g.
> > square, there’s likely a simple variant which will work.
> >
> >
> >
> > In my experience mri_label2label –dilate takes a lot of time and I’m
> > not sure you can restrict it to give you points on the surface that
> > you want.  I think it gives you a new surface which is displaced by a
> > fixed distance from the one where you start.
> >
> >
> >
> > I hope this is helpful.
> >
> >
> >
> > Best - Don
> >
> >
> >
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martha
> > Shiell
> > Sent: Saturday, February 13, 2016 12:59 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: [Freesurfer] Freesurfer tool to automatically generate label
> > surrounding a given vertex?
> >
> >
> >
> > Hello Freesurfer community,
> >
> >
> >
> > I am looking for a way to automatically generate a surface label file
> > of a specific dimension (e.g. a circle with a specific diameter, or a
> > square), given a specific vertex and some measure of the desired size.
> >
> >
> >
> > I have considered to do so by starting with a label file consisting of
> > a single vertex, and then expanding this label with the
> > mri_label2label tool, using the --dilate option. I wanted to know
> > though if anyone has any better suggestions.
> >
> >
> >
> > Thank you,
> >
> > Martha
> >
> >
> >
> > --
> >
> > Martha M. Shiell, PhD
> >
> >
> >

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Re: [Freesurfer] Freesurfer tool to automatically generate label surrounding a given vertex?

[Krieger, Donald N.]

Hi Martha,

A brute force but simple way to do this is to use the list of labels contained 
in subjects/nnn/label/lh.cortex and rh.cortex.
Given a vertex x,y,z, go through the file and select the lines for which the 
distance to x,y,z <= 2 mm.  This will give you a bunch of labels for points 
within a circle with 2 mm radius about x,y,z.  And all of them will be on the 
“white” surface.  If your vertex is on a different surface, e.g. pia, or you 
want a different geometry, e.g. square, there’s likely a simple variant which 
will work.

In my experience mri_label2label –dilate takes a lot of time and I’m not sure 
you can restrict it to give you points on the surface that you want.  I think 
it gives you a new surface which is displaced by a fixed distance from the one 
where you start.

I hope this is helpful.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martha Shiell
Sent: Saturday, February 13, 2016 12:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer tool to automatically generate label 
surrounding a given vertex?

Hello Freesurfer community,

I am looking for a way to automatically generate a surface label file of a 
specific dimension (e.g. a circle with a specific diameter, or a square), given 
a specific vertex and some measure of the desired size.

I have considered to do so by starting with a label file consisting of a single 
vertex, and then expanding this label with the mri_label2label tool, using the 
--dilate option. I wanted to know though if anyone has any better suggestions.

Thank you,
Martha

--
Martha M. Shiell, PhD
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Re: [Freesurfer] difference in 001.mgz found

[Krieger, Donald N.]

Thanks for the confirmation, Bruce.
I've looked at  the other files I spot checked which failed to match.
A bunch of the files in directory surf contain a line at the top like "Created 
by nobody on Mon Feb 8 15:13:58 2016"
The mri/transforms/talairach.m3z.inv.?.mgz files contain the pathname of a  
.xfm file.
I'm pretty confident now that we are getting the same results from all the runs 
but I want write something to check systematically.

Best - Don

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, February 10, 2016 8:15 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] difference in 001.mgz found
> 
> yes, we store the command lines used to generate a .mgz in the header, so that
> makes sense Bruce On Thu, 11 Feb 2016, Krieger, Donald N. wrote:
> 
> > These runs were executed on the Open Science Grid.
> > So the data file, the scan, was uploaded to grid worker machine, placed in a
> transitory directory, and processed.
> > The full pathname of the file is included in 001.mgz.
> > I got it by: zcat mri/orig/001.mgz | strings Here are the input and
> > output file names for 2 of the runs:
> > /var/lib/condor/execute/dir_31034/MRN_1_defaced.mgz
> > /scratch/tmp.FFTGBhmgp8/MRN_1/mri/orig/001.mgz
> >
> > /var/lib/condor/execute/dir_3734674/glide_HRFaAm/execute/dir_3741395/M
> > RN_1_defaced.mgz /scratch/tmp.ghJfB4leGR/MRN_1/mri/orig/001.mgz
> >
> > Best - Don
> >
> >
> >> -Original Message-
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >> boun...@nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N.
> >> Sent: Wednesday, February 10, 2016 6:38 PM
> >> To: Freesurfer support list
> >> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> >>
> >> It looks like they do give the same results.
> >> I have to write something to go through everything systematically
> >> which I may not get to till tomorrow.
> >> Also I am checking to see whether there was some difference in how
> >> 001.mgz was created.
> >> The source image file on which we are running freesurfer is a defaced.mgz .
> >> It's possible that it was sitting in a different directory for the
> >> different runs since the runs were executed by a work flow management
> >> system (Pegasus) on the Open Science Grid.
> >>
> >> Don
> >>
> >> 
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
> >> boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> >> [gr...@nmr.mgh.harvard.edu]
> >> Sent: Wednesday, February 10, 2016 6:13 PM
> >> To: freesurfer@nmr.mgh.harvard.edu
> >> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> >>
> >> That probably means that there is something in the header that is
> >> different. It should print a report to the terminal. Do they not give the 
> >> same
> results?
> >>
> >> On 02/10/2016 04:36 PM, Krieger, Donald N. wrote:
> >>> mri_diff finds no differences in the mri/orig/001.mgz's but the
> >>> checksums are
> >> different.
> >>> In fact, their sizes are slightly different.
> >>>
> >>>
> >>>
> >>>> -Original Message-
> >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >>>> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> >>>> Sent: Wednesday, February 10, 2016 3:45 PM
> >>>> To: Freesurfer support list
> >>>> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> >>>>
> >>>> Hi Don
> >>>>
> >>>> are you saying the 001.mgz is different when created from the same
> >>>> dicom data? Can you run mri_diff on it to see what the difference is?
> >>>>
> >>>> cheers
> >>>> Bruce
> >>>> On Wed, 10
> >>>> Feb 2016, Krieger, Donald N. wrote:
> >>>>
> >>>>> We would like to confirm that we are getting identical results
> >>>>> from multiple freesurfer runs on the same data set.
> >>>>>
> >>>>> To do so we are comparing identically named files using md5sum and
> >>>>> would very much appreciate your thoughts on our results.  For
> >>>>> multiple files, we concat

[Freesurfer] difference in 001.mgz found

[Krieger, Donald N.]

These runs were executed on the Open Science Grid.
So the data file, the scan, was uploaded to grid worker machine, placed in a 
transitory directory, and processed.
The full pathname of the file is included in 001.mgz.
I got it by: zcat mri/orig/001.mgz | strings
Here are the input and output file names for 2 of the runs:
/var/lib/condor/execute/dir_31034/MRN_1_defaced.mgz 
/scratch/tmp.FFTGBhmgp8/MRN_1/mri/orig/001.mgz

/var/lib/condor/execute/dir_3734674/glide_HRFaAm/execute/dir_3741395/MRN_1_defaced.mgz
 /scratch/tmp.ghJfB4leGR/MRN_1/mri/orig/001.mgz

Best - Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N.
> Sent: Wednesday, February 10, 2016 6:38 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> 
> It looks like they do give the same results.
> I have to write something to go through everything systematically which I may
> not get to till tomorrow.
> Also I am checking to see whether there was some difference in how 001.mgz
> was created.
> The source image file on which we are running freesurfer is a defaced.mgz .
> It's possible that it was sitting in a different directory for the different 
> runs
> since the runs were executed by a work flow management system (Pegasus) on
> the Open Science Grid.
> 
> Don
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
> boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, February 10, 2016 6:13 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> 
> That probably means that there is something in the header that is different. 
> It
> should print a report to the terminal. Do they not give the same results?
> 
> On 02/10/2016 04:36 PM, Krieger, Donald N. wrote:
> > mri_diff finds no differences in the mri/orig/001.mgz's but the checksums 
> > are
> different.
> > In fact, their sizes are slightly different.
> >
> >
> >
> >> -Original Message-
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> >> Sent: Wednesday, February 10, 2016 3:45 PM
> >> To: Freesurfer support list
> >> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> >>
> >> Hi Don
> >>
> >> are you saying the 001.mgz is different when created from the same
> >> dicom data? Can you run mri_diff on it to see what the difference is?
> >>
> >> cheers
> >> Bruce
> >> On Wed, 10
> >> Feb 2016, Krieger, Donald N. wrote:
> >>
> >>> We would like to confirm that we are getting identical results from
> >>> multiple freesurfer runs on the same data set.
> >>>
> >>> To do so we are comparing identically named files using md5sum and
> >>> would very much appreciate your thoughts on our results.  For
> >>> multiple files, we concatenate them and pipe the output into md5sum.
> >>> Below is a table showing what we’ve found so far.  I take hope from
> >>> the positive matches we get from all of the .annot files and from
> >>> the fact that 001.mgz does not match.  This latter suggests that
> >>> there is a date or something embedded in some of the files from
> >>> separate runs which
> >> defeats the match.
> >>>
> >>>
> >>> Please let us know what you know about this and thanks.
> >>>
> >>>
> >>>
> >>> file(s)
> >>>
> >>> md5sum result
> >>>
> >>> label/*.annot
> >>>
> >>> match
> >>>
> >>> label/*.label
> >>>
> >>> match
> >>>
> >>> mri/wmparc.mgz
> >>>
> >>> mismatch
> >>>
> >>> surf/qsphere.nofix
> >>>
> >>> surf/rh.sphere
> >>>
> >>> mismatch
> >>>
> >>> mri/orig/001.mgz
> >>>
> >>> mismatch
> >>>
> >>> mri/transforms/talairach.m3z
> >>>
> >>> match
> >>>
> >>> mri/transforms/talairach.m3z.inv.x.mgz
> >>>
> >>> mri/transforms/talairach.m3z.inv.y.mgz
> >>>
> >>> mri/transforms/talairach.m3z.inv.z.mgz
> >>>
> >>> mismatch
> >

Re: [Freesurfer] comparing multiple runs on the same scan

[Krieger, Donald N.]

It looks like they do give the same results.
I have to write something to go through everything systematically which I may 
not get to till tomorrow.
Also I am checking to see whether there was some difference in how 001.mgz was 
created.
The source image file on which we are running freesurfer is a defaced.mgz . 
It's possible that it was sitting in a different directory for the different 
runs since the runs were executed by a work flow management system (Pegasus) on 
the Open Science Grid.

Don


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 10, 2016 6:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] comparing multiple runs on the same scan

That probably means that there is something in the header that is
different. It should print a report to the terminal. Do they not give
the same results?

On 02/10/2016 04:36 PM, Krieger, Donald N. wrote:
> mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are 
> different.
> In fact, their sizes are slightly different.
>
>
>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
>> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
>> Sent: Wednesday, February 10, 2016 3:45 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
>>
>> Hi Don
>>
>> are you saying the 001.mgz is different when created from the same dicom
>> data? Can you run mri_diff on it to see what the difference is?
>>
>> cheers
>> Bruce
>> On Wed, 10
>> Feb 2016, Krieger, Donald N. wrote:
>>
>>> We would like to confirm that we are getting identical results from
>>> multiple freesurfer runs on the same data set.
>>>
>>> To do so we are comparing identically named files using md5sum and
>>> would very much appreciate your thoughts on our results.  For multiple
>>> files, we concatenate them and pipe the output into md5sum.  Below is
>>> a table showing what we’ve found so far.  I take hope from the
>>> positive matches we get from all of the .annot files and from the fact
>>> that 001.mgz does not match.  This latter suggests that there is a
>>> date or something embedded in some of the files from separate runs which
>> defeats the match.
>>>
>>>
>>> Please let us know what you know about this and thanks.
>>>
>>>
>>>
>>> file(s)
>>>
>>> md5sum result
>>>
>>> label/*.annot
>>>
>>> match
>>>
>>> label/*.label
>>>
>>> match
>>>
>>> mri/wmparc.mgz
>>>
>>> mismatch
>>>
>>> surf/qsphere.nofix
>>>
>>> surf/rh.sphere
>>>
>>> mismatch
>>>
>>> mri/orig/001.mgz
>>>
>>> mismatch
>>>
>>> mri/transforms/talairach.m3z
>>>
>>> match
>>>
>>> mri/transforms/talairach.m3z.inv.x.mgz
>>>
>>> mri/transforms/talairach.m3z.inv.y.mgz
>>>
>>> mri/transforms/talairach.m3z.inv.z.mgz
>>>
>>> mismatch
>>>
>>> mismatch
>>>
>>> mismatch
>>>
>>>
>>>
>>> Best - Don
>>>
>>>
>>>
>>>
>>>
>>> Don Krieger, Ph.D.
>>>
>>> Department of Neurological Surgery
>>>
>>> University of Pittsburgh
>>>
>>>
>>>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] comparing multiple runs on the same scan

[Krieger, Donald N.]

mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are 
different.
In fact, their sizes are slightly different.



> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, February 10, 2016 3:45 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> 
> Hi Don
> 
> are you saying the 001.mgz is different when created from the same dicom
> data? Can you run mri_diff on it to see what the difference is?
> 
> cheers
> Bruce
> On Wed, 10
> Feb 2016, Krieger, Donald N. wrote:
> 
> >
> > We would like to confirm that we are getting identical results from
> > multiple freesurfer runs on the same data set.
> >
> > To do so we are comparing identically named files using md5sum and
> > would very much appreciate your thoughts on our results.  For multiple
> > files, we concatenate them and pipe the output into md5sum.  Below is
> > a table showing what we’ve found so far.  I take hope from the
> > positive matches we get from all of the .annot files and from the fact
> > that 001.mgz does not match.  This latter suggests that there is a
> > date or something embedded in some of the files from separate runs which
> defeats the match.
> >
> >
> >
> > Please let us know what you know about this and thanks.
> >
> >
> >
> > file(s)
> >
> > md5sum result
> >
> > label/*.annot
> >
> > match
> >
> > label/*.label
> >
> > match
> >
> > mri/wmparc.mgz
> >
> > mismatch
> >
> > surf/qsphere.nofix
> >
> > surf/rh.sphere
> >
> > mismatch
> >
> > mri/orig/001.mgz
> >
> > mismatch
> >
> > mri/transforms/talairach.m3z
> >
> > match
> >
> > mri/transforms/talairach.m3z.inv.x.mgz
> >
> > mri/transforms/talairach.m3z.inv.y.mgz
> >
> > mri/transforms/talairach.m3z.inv.z.mgz
> >
> > mismatch
> >
> > mismatch
> >
> > mismatch
> >
> >
> >
> > Best - Don
> >
> >
> >
> >
> >
> > Don Krieger, Ph.D.
> >
> > Department of Neurological Surgery
> >
> > University of Pittsburgh
> >
> >
> >

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Re: [Freesurfer] comparing multiple runs on the same scan

[Krieger, Donald N.]

Thanks very much for getting back so quickly.
Please pardon.
I’m sure this answer must be in lots of other places.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of dgw
Sent: Wednesday, February 10, 2016 3:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] comparing multiple runs on the same scan

Doug responded to your previous mail with this:

Even on the same operating system they will be different because there
is stuff in the header that will change. Use mri_diff (volumes,
segmentations, and surface overlays) or mris_diff for surfaces to check
whether they are different.
[Image removed by sender.]
hth
d


On Wed, Feb 10, 2016 at 2:14 PM, Krieger, Donald N. 
mailto:krieg...@upmc.edu>> wrote:
We would like to confirm that we are getting identical results from multiple 
freesurfer runs on the same data set.
To do so we are comparing identically named files using md5sum and would very 
much appreciate your thoughts on our results.  For multiple files, we 
concatenate them and pipe the output into md5sum.  Below is a table showing 
what we’ve found so far.  I take hope from the positive matches we get from all 
of the .annot files and from the fact that 001.mgz does not match.  This latter 
suggests that there is a date or something embedded in some of the files from 
separate runs which defeats the match.

Please let us know what you know about this and thanks.

file(s)

md5sum result

label/*.annot

match

label/*.label

match

mri/wmparc.mgz

mismatch

surf/qsphere.nofix
surf/rh.sphere

mismatch

mri/orig/001.mgz

mismatch

mri/transforms/talairach.m3z

match

mri/transforms/talairach.m3z.inv.x.mgz
mri/transforms/talairach.m3z.inv.y.mgz
mri/transforms/talairach.m3z.inv.z.mgz

mismatch
mismatch
mismatch


Best - Don


Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

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[Freesurfer] comparing multiple runs on the same scan

[Krieger, Donald N.]

We would like to confirm that we are getting identical results from multiple 
freesurfer runs on the same data set.
To do so we are comparing identically named files using md5sum and would very 
much appreciate your thoughts on our results.  For multiple files, we 
concatenate them and pipe the output into md5sum.  Below is a table showing 
what we've found so far.  I take hope from the positive matches we get from all 
of the .annot files and from the fact that 001.mgz does not match.  This latter 
suggests that there is a date or something embedded in some of the files from 
separate runs which defeats the match.

Please let us know what you know about this and thanks.

file(s)

md5sum result

label/*.annot

match

label/*.label

match

mri/wmparc.mgz

mismatch

surf/qsphere.nofix
surf/rh.sphere

mismatch

mri/orig/001.mgz

mismatch

mri/transforms/talairach.m3z

match

mri/transforms/talairach.m3z.inv.x.mgz
mri/transforms/talairach.m3z.inv.y.mgz
mri/transforms/talairach.m3z.inv.z.mgz

mismatch
mismatch
mismatch


Best - Don


Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
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[Freesurfer] spot checking results

[Krieger, Donald N.]

Dear List,

I have run recon-all -all on the same scan on two different machines likely 
running two different versions of Linux but in any case the runs were done with 
different numbers of cores.
I  haven't done anything fancy to compare that the results are identical except 
for some spot checks of individual files with md5sum.
label/lh.BA4a.label shows up the same on both.
mri/wmparc.mgz does not.
Your comments would be welcome.
Is there something about the non-ascii files, e.g. wmparc.mgz, which would make 
them show different checksums, e.g. inclusion of a processing time or some such?
Do you have experience or suggestions for convincing ourselves that we are 
getting the same answers on different machines?
???

Thanks - Don

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[Freesurfer] visualization of a "spherical" cut

[Krieger, Donald N.]

Dear List,

I have a visualization problem which is not directly relevant to freesurfer but 
which may be easily solvable with the freesurfer tools.
I have also posted this question to the ImageJ discussion list.

I would like to visualize "spherical" cuts through an MR.
An axial cut is the intersection of the image volume with a plane normal to a 
line running superior to inferior through the volume.
A spherical cut is the intersection of a sphere with specified  origin through 
the volume.
Hence the visual would be a disc with radius that of the sphere and center at 
the origin.
There would be two such discs, one for the front and one for the back.

What do you think?
Is there an easy way?
Any thought and/or suggestions would be welcome.

Thanks - Don

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Re: [Freesurfer] example #PBS Torque script for FreeSurfer on a HPC cluster & multithreading question

[Krieger, Donald N.]

Hi Joost -

Here's my understanding which comes from limited experience with PBS and SLURM.
Your master process is a bash, tcsh, or other shell script with PBS directives 
embedded in it.
Each recon-all command within your script should include a -openmp N switch 
which specifies the number of the threads you want to use for that freesurfer 
run.
It looks like you get a total of 32 threads per core.
Since a typical recon-all -all run will use multiple threads about 30% of the 
time, you must over-subscribe the number of threads to which you have access to 
use them efficiently.
You have two key parameters to choose:

(1)   #threads for each freesurfer run: I suggest 8.

(2)   #simultaneous freesurfer instances running at any one time: I suggest 
starting with 10, i.e. 10 x 8 = 80 threads requested.
You also have the problem of sensing when one of your freesurfer runs completes 
and starting another to keep 10 recon-all -all instances running.  You can use 
the recon-all switch -notify to create a "completed" file for each freesurfer 
run and poll and count those files to decide when to spawn additional instances 
of recon-all.

I hope this is helpful.   I think it would be interesting and valuable to hear 
what your experience is with this in whatever detail you can provide.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Riphagen Joost (NP)
Sent: Wednesday, December 16, 2015 6:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] example #PBS Torque script for FreeSurfer on a HPC 
cluster & multithreading question


Dear all,



I'm learning  how to work with Freesurfer on a #PBS/Torque  HPC cluster. There 
is enough documentation about using #PBS, but I have not been able to find 
anything on the net about how to process multiple subjects in FS in this 
environment.

If somebody is willing to share an example script that would be most helpful.



Am I right in thinking that by using the "-itkthreads" flag FS can make use of 
multiple threads but not use multiple cores ?

The nodes use two Xeon processors with 8 cores and 16 threads per CPU and have 
64 GB per node.  I have to book per node so the more I can use it the better.





Regards



Joost Riphagen










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Re: [Freesurfer] direction for restart in the middle

[Krieger, Donald N.]

Thanks, Bruce. - Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, November 18, 2015 8:55 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] direction for restart in the middle
> 
> Hi Don
> 
> the defect is too big to fix, and probably means something dramatic is wrong
> (e.g. skull or cerebellum attached to the brain component of the wm.mgz).
> Check out the ?h.inflated.nofix and see what is going on and correct it before
> rerunning
> 
> cheers
> Bruce
> On Wed, 18 Nov 2015, Krieger, Donald N. wrote:
> 
> >
> > I have run freesurfer 6Beta on the scan with very large CSF spaces
> >
> > With flags: -bigventricles and –notal-check .
> >
> > I used the latter flag per suggestions in the log as the first run
> > failed on a talaraich check.
> >
> > This second run appears to be hung as it has not written anything new
> > into the recon-all.log file for 7 hours.
> >
> > I would like to restart this at a reasonable point rather than at the
> > beginning.
> >
> > Can you recognize where it is and what is are suggested restart flags?
> >
> >
> >
> > Here are the files which have appeared in the mri directory.
> >
> > aseg.auto.mgz   aseg.presurf.mgz   brainmask.mgz  error.log
> > mri_nu_correct.mni.log.bak  nu_noneck.mgz  orig_nu.log  segment.dat
> >  talairach.log   transforms   wm.mgz
> >
> > aseg.auto_noCCseg.label_intensities.txt  brain.finalsurfs.mgz
> > brain.mgz  filled.mgz  norm.mgz orig
> > orig_nu.mgz  T1.mgz talairach_with_skull_2.log  v.mgz
> > wm.seg.mgz
> >
> > aseg.auto_noCCseg.mgz    brainmask.auto.mgz
> > ctrl_pts.mgz   mri_nu_correct.mni.log  nu.mgz orig.mgz
> > rawavg.mgz   talairach.label_intensities.txt talairach_with_skull.log
> > wm.asegedit.mgz
> >
> >
> >
> > Here are the last 50 lines or so of the log file:
> >
> > ProgramName: mri_ca_normalize  ProgramArguments: -all-
> info  ProgramVersion:
> > $Name: stable5 $  TimeStamp: 2
> >
> > ion: 3.10.73-1.el6.elrepo.x86_64  CompilerName: GCC  CompilerVersion:
> > 40400
> >
> > ...skipping...
> >
> > mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 lh
> >
> >
> >
> > reading spherical homeomorphism from 'qsphere.nofix'
> >
> > using genetic algorithm with optimized parameters
> >
> > setting seed for random number genererator to 1234
> >
> >
> >
> > *
> >
> > Topology Correction Parameters
> >
> > retessellation mode:   genetic search
> >
> > number of patches/generation : 10
> >
> > number of generations :    10
> >
> > surface mri loglikelihood coefficient : 1.0
> >
> > volume mri loglikelihood coefficient :  10.0
> >
> > normal dot loglikelihood coefficient :  1.0
> >
> > quadratic curvature loglikelihood coefficient : 1.0
> >
> > volume resolution : 2
> >
> > eliminate vertices during search :  1
> >
> > initial patch selection :   1
> >
> > select all defect vertices :    0
> >
> > ordering dependant retessellation:  0
> >
> > use precomputed edge table :    0
> >
> > smooth retessellated patch :    2
> >
> > match retessellated patch : 1
> >
> > verbose mode :  0
> >
> >
> >
> > *
> >
> > INFO: assuming .mgz format
> >
> > $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
> >
> >   $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $
> >
> > before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556,
> > g=256)
> >
> > using quasi-homeomorphic spherical map to tessellate cortical surface...
> >
> >
> >
> > Correction of the Topology
> >
> > Finding true center and radius of Spherical Surface...done
> >
> > Surface centered at (0,0,0) with radius 100.0 in 10 iterations
> >
> > marking ambiguous vertices...
> >
> > 111330 ambiguous faces found in tessellation
> >
> > segmenting defects...
> >
> &

[Freesurfer] direction for restart in the middle

[Krieger, Donald N.]

I have run freesurfer 6Beta on the scan with very large CSF spaces
With flags: -bigventricles and -notal-check .
I used the latter flag per suggestions in the log as the first run failed on a 
talaraich check.
This second run appears to be hung as it has not written anything new into the 
recon-all.log file for 7 hours.
I would like to restart this at a reasonable point rather than at the beginning.
Can you recognize where it is and what is are suggested restart flags?

Here are the files which have appeared in the mri directory.
aseg.auto.mgz   aseg.presurf.mgz   brainmask.mgz  error.log
mri_nu_correct.mni.log.bak  nu_noneck.mgz  orig_nu.log  segment.dat  
talairach.log   transforms   wm.mgz
aseg.auto_noCCseg.label_intensities.txt  brain.finalsurfs.mgz  brain.mgz  
filled.mgz  norm.mgzorig   orig_nu.mgz  
T1.mgz   talairach_with_skull_2.log  v.mgz
wm.seg.mgz
aseg.auto_noCCseg.mgzbrainmask.auto.mgzctrl_pts.mgz   
mri_nu_correct.mni.log  nu.mgz  orig.mgz   rawavg.mgz   
talairach.label_intensities.txt  talairach_with_skull.logwm.asegedit.mgz

Here are the last 50 lines or so of the log file:
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2
ion: 3.10.73-1.el6.elrepo.x86_64  CompilerName: GCC  CompilerVersion: 40400
...skipping...
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 lh

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*
Topology Correction Parameters
retessellation mode:   genetic search
number of patches/generation : 10
number of generations :10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient :  10.0
normal dot loglikelihood coefficient :  1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution : 2
eliminate vertices during search :  1
initial patch selection :   1
select all defect vertices :0
ordering dependant retessellation:  0
use precomputed edge table :0
smooth retessellated patch :2
match retessellated patch : 1
verbose mode :  0

*
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
  $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $
before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556, g=256)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
111330 ambiguous faces found in tessellation
segmenting defects...
38 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
  -merging segment 13 into 0
  -merging segment 23 into 0
  -merging segment 29 into 0
  -merging segment 32 into 0
  -merging segment 36 into 0
  -merging segment 16 into 12
  -merging segment 15 into 14
31 defects to be corrected
0 vertices coincident
reading input surface 
/oasis/scratch/comet/donkri/temp_project/subjects/201/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
  -face   loglikelihood: -9.2710  (-4.6355)
  -vertex loglikelihood: -8.2866  (-4.1433)
  -normal dot loglikelihood: -3.4816  (-3.4816)
  -quad curv  loglikelihood: -6.0138  (-3.0069)
  Total Loglikelihood : -27.0531

CORRECTING DEFECT 0 (vertices=53053, convex hull=8873)

Thanks for your direction on this.  - Don

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Re: [Freesurfer] grossly abormal brain

[Krieger, Donald N.]

Thanks very much, Bruce.
I have 6Beta running now with -bigventricles and -fingerscrossed.

Thanks very much, Anthony, for the reference.
I'll fetch it and see what I can do as that approach is interesting from 
several angles for our work.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anthony Dick
Sent: Tuesday, November 17, 2015 9:12 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] grossly abormal brain

Don, if that doesn't work, try the procedure outlined in this paper, although 
it is rather involved: 
http://www.architalbiol.org/index.php/aib/article/viewArticle/1221

Anthony

On 11/17/15 8:27 AM, Bruce Fischl wrote:
Hi Don

it's impossible to say. Certainly 6.0 will be your best bet as it handles 
enlarged ventricles much better. Try 6.0 beta with the -bigventricles flag and 
see how it goes

cheers
Bruce
On Tue, 17 Nov 2015, Krieger, Donald N. wrote:



A few cuts from a grossly abnormal scan are attached.

Do you think freesurfer can effectively segment this one?

If so, please point us in the right direction to get started with it.

Thanks. - Don








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--

Anthony Steven Dick, Ph.D.

Assistant Professor

Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience

Department of Psychology

Florida International University Modesto A. Maidique Campus AHC4 454

11200 S.W. 8th Street

Miami, FL 33199

Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879

Email: ad...@fiu.edu<mailto:ad...@fiu.edu>

Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu

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[Freesurfer] grossly abormal brain

[Krieger, Donald N.]

A few cuts from a grossly abnormal scan are attached.
Do you think freesurfer can effectively segment this one?
If so, please point us in the right direction to get started with it.
Thanks. - Don

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[Freesurfer] very large csf spaces

[Krieger, Donald N.]

This is a newbie question as this is the first grossly abnormal scan on which I 
need to run freesurfer.
There are very large CSF spaces and only a rim of cortex and white matter for 
many regions.
Freesurfer fails very early on.
Before I post errors, I would like to try to get it to complete if there are 
pointers online.

Is there a tutorial for running freesurfer on a grossly abnormal scan?
Are  there standard rules of thumb?
Thanks - Don
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Re: [Freesurfer] list of normals to triangle vertices

[Krieger, Donald N.]

Thank you very much.

Best regards,
 
Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Tuesday, October 13, 2015 10:51 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] list of normals to triangle vertices
> 
> Hi Don
> 
> 1. I think so, yes.
> 2. Yes.
> 3. The convention is that they point outwards from wm->ctx 4. Yes.
> 
> On Tue, 13 Oct 2015, Krieger, Donald N. wrote:
> 
> > Thanks very much, Bruce.
> > That saves me a ton of effort.
> >
> > Let me confirm a few key details.
> > The command with -n kicks out a file with 2 header lines, a list of normals,
> and a list of triangles for which each is defined by its 3 vertex numbers.
> > I see the format for a "Triangle Surface File - ASCII version" on Graham
> Wideman's web pages created many moons ago:
> > http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm#Triang
> > leASCII
> >
> > Can you point me to more up-to-date and detailed info, perhaps on the
> > wiki? (1) Are the normals in TkRAS coordinates?  I can check this
> > pretty easily.  Please pardon my laziness in asking. (2) The list of
> > normals I presume are in order beginning at vertex number zero??  I
> > would like to make sure I identify the correct vertex number for each
> > normal.  How? (3) Are the normals consistently pointing one way, e.g.
> > ctx --> wm? (4) Is the order of the vertex numbers for each triangle
> > consistent to provide reliable ctx --> wm directionality.  If so is it
> > (v1-v2)X(v2-v3) or vica versa?
> >
> > Best regards,
> >
> > Don
> >
> >> -Original Message-
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> >> Sent: Tuesday, October 13, 2015 8:45 AM
> >> To: Freesurfer support list
> >> Subject: Re: [Freesurfer] list of normals to triangle vertices
> >>
> >> Hi Don
> >>
> >> mris_convert -n lh.white lh.white.normals.asc
> >>
> >> should do the trick. And this is the way that the area is computed
> >> (from
> >> mrisurf.c):
> >>
> >> static float
> >> mrisTriangleArea(MRIS *mris, int fac, int n) {
> >>int n0,n1;
> >>face_type *f;
> >>float v0[3],v1[3],d1,d2,d3;
> >>
> >>n0 = (n == 0)   ? VERTICES_PER_FACE-1 : n-1;
> >>n1 = (n == VERTICES_PER_FACE-1) ? 0   : n+1;
> >>f = &mris->faces[fac];
> >>v0[0] = mris->vertices[f->v[n]].x - mris->vertices[f->v[n0]].x;
> >>v0[1] = mris->vertices[f->v[n]].y - mris->vertices[f->v[n0]].y;
> >>v0[2] = mris->vertices[f->v[n]].z - mris->vertices[f->v[n0]].z;
> >>v1[0] = mris->vertices[f->v[n1]].x - mris->vertices[f->v[n]].x;
> >>v1[1] = mris->vertices[f->v[n1]].y - mris->vertices[f->v[n]].y;
> >>v1[2] = mris->vertices[f->v[n1]].z - mris->vertices[f->v[n]].z;
> >>d1 = -v1[1]*v0[2] + v0[1]*v1[2];
> >>d2 = v1[0]*v0[2] - v0[0]*v1[2];
> >>d3 = -v1[0]*v0[1] + v0[0]*v1[1];
> >>return sqrt(d1*d1+d2*d2+d3*d3)/2;
> >> }
> >>
> >>
> >>
> >> cheers
> >> Bruce
> >>
> >>
> >> On Tue, 13 Oct 2015, Krieger, Donald N. wrote:
> >>
> >>>
> >>> Hi everyone,
> >>>
> >>>
> >>>
> >>> I need to create the vector normal to the surface at each “white” vertex.
> >>>
> >>> I would like to end up with 7 fields in each entry:
> >>>
> >>> 1 Vertex number
> >>>
> >>> 2-4  RAS coordinates
> >>>
> >>> 5-7 RAS components of the normal vector pointed from ctx à wm
> >>>
> >>>
> >>>
> >>> mri_annotation2label gets me the first 4.
> >>>
> >>> I just don’t want to reinvent the wheel getting the normal.
> >>>
> >>> If there’s a way to get freesurfer to kick out the normals, that
> >>> would be best.
> >>>
> >>> Here are naïve questions that arise out of this problem:
> >>>
> >>> 1.   Is there a simple way to identify which vertices are
> >>> “nearest neighbors” other than measuring and sorting the distances
> >>> between each

Re: [Freesurfer] list of normals to triangle vertices

[Krieger, Donald N.]

Thanks very much, Bruce.
That saves me a ton of effort.

Let me confirm a few key details.
The command with -n kicks out a file with 2 header lines, a list of normals, 
and a list of triangles for which each is defined by its 3 vertex numbers.
I see the format for a "Triangle Surface File - ASCII version" on Graham 
Wideman's web pages created many moons ago:
http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm#TriangleASCII

Can you point me to more up-to-date and detailed info, perhaps on the wiki?
(1) Are the normals in TkRAS coordinates?  I can check this pretty easily.  
Please pardon my laziness in asking.
(2) The list of normals I presume are in order beginning at vertex number 
zero??  I would like to make sure I identify the correct vertex number for each 
normal.  How?
(3) Are the normals consistently pointing one way, e.g. ctx --> wm?
(4) Is the order of the vertex numbers for each triangle consistent to provide 
reliable ctx --> wm directionality.  If so is it (v1-v2)X(v2-v3) or vica versa? 
  

Best regards,
 
Don

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Tuesday, October 13, 2015 8:45 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] list of normals to triangle vertices
> 
> Hi Don
> 
> mris_convert -n lh.white lh.white.normals.asc
> 
> should do the trick. And this is the way that the area is computed (from
> mrisurf.c):
> 
> static float
> mrisTriangleArea(MRIS *mris, int fac, int n) {
>int n0,n1;
>face_type *f;
>float v0[3],v1[3],d1,d2,d3;
> 
>n0 = (n == 0)   ? VERTICES_PER_FACE-1 : n-1;
>n1 = (n == VERTICES_PER_FACE-1) ? 0   : n+1;
>f = &mris->faces[fac];
>v0[0] = mris->vertices[f->v[n]].x - mris->vertices[f->v[n0]].x;
>v0[1] = mris->vertices[f->v[n]].y - mris->vertices[f->v[n0]].y;
>v0[2] = mris->vertices[f->v[n]].z - mris->vertices[f->v[n0]].z;
>v1[0] = mris->vertices[f->v[n1]].x - mris->vertices[f->v[n]].x;
>v1[1] = mris->vertices[f->v[n1]].y - mris->vertices[f->v[n]].y;
>v1[2] = mris->vertices[f->v[n1]].z - mris->vertices[f->v[n]].z;
>d1 = -v1[1]*v0[2] + v0[1]*v1[2];
>d2 = v1[0]*v0[2] - v0[0]*v1[2];
>d3 = -v1[0]*v0[1] + v0[0]*v1[1];
>return sqrt(d1*d1+d2*d2+d3*d3)/2;
> }
> 
> 
> 
> cheers
> Bruce
> 
> 
> On Tue, 13 Oct 2015, Krieger, Donald N. wrote:
> 
> >
> > Hi everyone,
> >
> >
> >
> > I need to create the vector normal to the surface at each “white” vertex.
> >
> > I would like to end up with 7 fields in each entry:
> >
> > 1 Vertex number
> >
> > 2-4  RAS coordinates
> >
> > 5-7 RAS components of the normal vector pointed from ctx à wm
> >
> >
> >
> > mri_annotation2label gets me the first 4.
> >
> > I just don’t want to reinvent the wheel getting the normal.
> >
> > If there’s a way to get freesurfer to kick out the normals, that would
> > be best.
> >
> > Here are naïve questions that arise out of this problem:
> >
> > 1.   Is there a simple way to identify which vertices are “nearest
> > neighbors” other than measuring and sorting the distances between each
> > and all the others i.e. which ones form a triangle?  I understand to
> > use the normalized average of the 6 triangles which include the vertex.
> >
> > 2.   Is there a simple way to identify the order of the sides of
> > each triangle so that their cross product is ordered correctly to
> > produce ctx à wm?
> >
> >
> >
> > Thanks for your help with this.
> >
> >
> >
> > Don
> >
> >
> >
> >
> >

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[Freesurfer] list of normals to triangle vertices

[Krieger, Donald N.]

Hi everyone,

I need to create the vector normal to the surface at each "white" vertex.
I would like to end up with 7 fields in each entry:

1 Vertex number
2-4  RAS coordinates
5-7 RAS components of the normal vector pointed from ctx --> wm

mri_annotation2label gets me the first 4.
I just don't want to reinvent the wheel getting the normal.
If there's a way to get freesurfer to kick out the normals, that would be best.
Here are naïve questions that arise out of this problem:

1.   Is there a simple way to identify which vertices are "nearest 
neighbors" other than measuring and sorting the distances between each and all 
the others i.e. which ones form a triangle?  I understand to use the normalized 
average of the 6 triangles which include the vertex.

2.   Is there a simple way to identify the order of the sides of each 
triangle so that their cross product is ordered correctly to produce ctx --> wm?

Thanks for your help with this.

Don

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Re: [Freesurfer] wm- volume limitations

[Krieger, Donald N.]

Great - just what I was looking for - thanks.

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Tuesday, July 07, 2015 10:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] wm- volume limitations


the wmparc gets the cortical parcellation of the closest cortical parcellation 
(not necessarily normal to the surface). I think it has to be within 5mm of 
cortex or else it gets "Unsegmented White Matter". The method is described here

http://www.ncbi.nlm.nih.gov/pubmed/19027860



On 7/7/15 8:36 PM, Krieger, Donald N. wrote:
Freesurfer provides ctx- and wm- volumes on either side of the "white" labelled 
sheet, all for a particular cortical region.
What is the idea which is used to limit the extent of the wm- volume which is 
adjacent to a particular ctx- volume?
Is it as simple as a maximum distance normal to  the white matter sheet?
I'm sure this is documented somewhere but I haven't been able to find it.
Thanks.

Don





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[Freesurfer] wm- volume limitations

[Krieger, Donald N.]

Freesurfer provides ctx- and wm- volumes on either side of the "white" labelled 
sheet, all for a particular cortical region.
What is the idea which is used to limit the extent of the wm- volume which is 
adjacent to a particular ctx- volume?
Is it as simple as a maximum distance normal to  the white matter sheet?
I'm sure this is documented somewhere but I haven't been able to find it.
Thanks.

Don

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521 on ubuntu 14.04 crash with Illegal instruction (core dumped)

[Krieger, Donald N.]

Thanks, Zeke.
If you have to remake it, it would be great if the executables were static.
But in any case I'll give it a try. -- Thanks.

Regards,
 
Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
> Sent: Sunday, May 24, 2015 5:48 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521 on
> ubuntu 14.04 crash with Illegal instruction (core dumped)
> 
> I will make it available to you and send you a link on Tuesday.
> 
> -Zeke
> 
> 
> > On May 23, 2015, at 10:48 AM, Krieger, Donald N. 
> wrote:
> >
> > Hi Zeke,
> >
> > I would like to try that version on comet to see if I get a significant 
> > speed-up.
> > Can you provide an address and pathname from which I can use wget to grab
> it?
> > I'll report back with results compared with the standard release.
> > Thanks,
> >
> > Don
> >
> > Don Krieger, Ph.D.
> > Department of Neurological Surgery
> > University of Pittsburgh
> >
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Z K
> > [zkauf...@nmr.mgh.harvard.edu]
> > Sent: Friday, May 22, 2015 12:06 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521
> > on ubuntu 14.04 crash with Illegal instruction (core dumped)
> >
> > That particular developmental build is compiled with optimization
> > flags for machines containing Intels new Haswell processor and wont
> > run on platforms without it. Although that build is available via our
> > dev download page, it remains an unsupported build that exists
> > primarily for internal experimental purposes only.
> >
> > -Zeke
> >
> >> On 05/22/2015 11:49 AM, Knut J Bjuland wrote:
> >> Hi
> >>
> >> I have tired the freesurfer-Linux-centos7_x86_64-dev-20150521. When I
> >> start mri_convert on ubuntu 14.04.4 I get this results.
> >>
> >> knutjb@dmed4960:/usr/local/freesurfer60$ export FREESURFER_HOME=
> >> /usr/local/freesurfer60
> >> knutjb@dmed4960:/usr/local/freesurfer60$ source
> >> /usr/local/freesurfer60/SetUpFreeSurfer.sh
> >>  freesurfer-Linux-centos7_x86_64-dev-20150521 
> >> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> >> FREESURFER_HOME   /usr/local/freesurfer60
> >> FSFAST_HOME   /usr/local/freesurfer/fsfast
> >> FSF_OUTPUT_FORMAT nii.gz
> >> SUBJECTS_DIR  /home/knutjb/subjects
> >> MNI_DIR   /usr/local/freesurfer/mni
> >> FSL_DIR   /usr/share/fsl/5.0
> >> knutjb@dmed4960:/usr/local/freesurfer60$ mri_con
> >> mri_concatmri_concatenate_lta   mri_convert_crash
> >> mri_concatenate_gcam  mri_convert   mri_convert_mdh
> >> knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert --help Illegal
> >> instruction (core dumped) knutjb@dmed4960:/usr/local/freesurfer60$
> >> mri_convert -h Illegal instruction (core dumped)
> >> knutjb@dmed4960:/usr/local/freesurfer60$
> >>
> >> and in GDB
> >> Starting program: /usr/local/freesurfer60/bin/mri_convert
> >> [Thread debugging using libthread_db enabled] Using host libthread_db
> >> library "/lib/x86_64-linux-gnu/libthread_db.so.1".
> >>
> >> Program received signal SIGILL, Illegal instruction.
> >> 0x006be48f in make_cmd_version_string (argc=argc@entry=1,
> >> argv=argv@entry=0x7fffdd98,
> >> id_string=id_string@entry=0xc6de08 "$Id: mri_convert.c,v 1.221
> >> 2015/04/16 18:56:00 greve Exp $",
> >> version_string=version_string@entry=0xc6cd66 "$Name:  $",
> >> return_string=return_string@entry=0x7fffb0e0 "(\rW\366\377\177")
> >> at version.c:215
> >> 215version.c: No such file or directory.
> >>
> >> Knut Jørgen Bjuland
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > ___
> > Freesurfer ma

Re: [Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521 on ubuntu 14.04 crash with Illegal instruction (core dumped)

[Krieger, Donald N.]

Hi Zeke,

I would like to try that version on comet to see if I get a significant 
speed-up.
Can you provide an address and pathname from which I can use wget to grab it?
I'll report back with results compared with the standard release.
Thanks,

Don

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Z K 
[zkauf...@nmr.mgh.harvard.edu]
Sent: Friday, May 22, 2015 12:06 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521 on 
ubuntu 14.04 crash with Illegal instruction (core dumped)

That particular developmental build is compiled with optimization flags
for machines containing Intels new Haswell processor and wont run on
platforms without it. Although that build is available via our dev
download page, it remains an unsupported build that exists primarily for
internal experimental purposes only.

-Zeke

On 05/22/2015 11:49 AM, Knut J Bjuland wrote:
> Hi
>
> I have tired the freesurfer-Linux-centos7_x86_64-dev-20150521. When I
> start mri_convert on ubuntu 14.04.4 I get this results.
>
> knutjb@dmed4960:/usr/local/freesurfer60$ export FREESURFER_HOME=
> /usr/local/freesurfer60
> knutjb@dmed4960:/usr/local/freesurfer60$ source
> /usr/local/freesurfer60/SetUpFreeSurfer.sh
>  freesurfer-Linux-centos7_x86_64-dev-20150521 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /usr/local/freesurfer60
> FSFAST_HOME   /usr/local/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /home/knutjb/subjects
> MNI_DIR   /usr/local/freesurfer/mni
> FSL_DIR   /usr/share/fsl/5.0
> knutjb@dmed4960:/usr/local/freesurfer60$ mri_con
> mri_concatmri_concatenate_lta   mri_convert_crash
> mri_concatenate_gcam  mri_convert   mri_convert_mdh
> knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert --help
> Illegal instruction (core dumped)
> knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert -h
> Illegal instruction (core dumped)
> knutjb@dmed4960:/usr/local/freesurfer60$
>
> and in GDB
> Starting program: /usr/local/freesurfer60/bin/mri_convert
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
>
> Program received signal SIGILL, Illegal instruction.
> 0x006be48f in make_cmd_version_string (argc=argc@entry=1,
>  argv=argv@entry=0x7fffdd98,
>  id_string=id_string@entry=0xc6de08 "$Id: mri_convert.c,v 1.221
> 2015/04/16 18:56:00 greve Exp $",
>  version_string=version_string@entry=0xc6cd66 "$Name:  $",
>  return_string=return_string@entry=0x7fffb0e0 "(\rW\366\377\177")
>  at version.c:215
> 215version.c: No such file or directory.
>
> Knut Jørgen Bjuland
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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>
>
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Re: [Freesurfer] problem with left/right parallelization

[Krieger, Donald N.]

Thanks for getting back.
The patched mri_segstats works.

Here are the results of our benchmark runs.
Each result comes from a single run so the precision is questionable.
But it seems clear that 8 processors makes little difference compared with 4.
And parallelizing by side also makes little difference.

I've included the scripts both for the simple runs, i.e. recon-all -all, and 
the parallized run.
The cores were Haswell processors with lots of local memory.

Serial run (4 cores): 5.465 hours
Serial run (8 cores): 5.251 hours
Parallel run (8 cores): 5.197 hours
The parallel run broke out as follows:
autorecon1(8 cores):0.189 hours
autorecon2-volonly (8 cores):   1.136 hours
2  autorecon2-perhemi (4 cores): 0.745/0.659 hours
It was the longer of these which was used for the total run time of 5.197 hours
autorecon3:   3.127 hours
recon-all -autorecon3 includes no executables which use multiple cores.

Regards,
 
Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
> Sent: Friday, May 01, 2015 5:38 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] problem with left/right parallelization
> 
> Yup this is a known issue with the mri_segstats binary.
> 
> Please go to the following page and download the mri_segstats file that
> corresponds to your version of freesurfer (see contents of
> $FREESURFER_HOME/build-stampt.txt file to determine your version).
> Replace the version of mri_segstats in your $FREESURFER_HOME/bin directory
> with the one you download from the following link. Also, it would be good to
> backup the version you currently have.
> 
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
> 
> -Zeke
> 
> On 05/01/2015 05:02 PM, Krieger, Donald N. wrote:
> > I have completed runs of recon-all -autorecon1 and recon-all
> > -autorecon2-volonly per your suggested sequence:
> >
> > recon-all -s subj -autorecon1
> >
> > recon-all -s subj -autorecon2-volonly
> >
> > recon-all -s subj -autorecon2-perhemi -hemi rh -log recon-all-hemi
> > rh.log -notify rh-done.log -openmp 4 &
> >
> > recon-all -s subj -autorecon2-perhemi -hemi lh -log
> > recon-all-hemi-lh.log -notify lh-done.log -openmp 4 &
> >
> > while (rh-done.log AND lh-done.log do not both exist)
> >
> > do
> >
> > sleep 1
> >
> > end loop
> >
> > recon-all -s -autorecon3
> >
> > recon-all -s subj -autorecon2-volonly is completing but with an error.
> >
> > I've included below my signature the last 50 lines or so of
> > recon-all.log (file attached).
> >
> > It looks like it's completing execution of mri_fill successfully and
> > then going on to execute mri_segstats out of order.
> >
> > In the log for a standard run on this same image set, i.e. recon-all
> > -all, that mri_segstats cmd doesn't appear to occur till 3000 lines
> > later in the log file.  And as the log file shows, no ribbon.mgz can
> > be found and inspection of the directories shows that surf is empty.
> >
> > It looks like something is missing between recon-all
> > -autorecon2-volonly and recon-all -autorecon2-perhemi
> >
> > What do you think?
> >
> > Thanks,
> >
> > Don
> >
> > Don Krieger, Ph.D.
> >
> > Department of Neurological Surgery
> >
> > Universityof Pittsburgh
> >
> > mri_pretess done
> >
> > #
> >
> > #@# Fill Fri May  1 12:28:01 PDT 2015
> >
> > /home/donkri/Contrib/freesurfer/subjects/173_9sh_lr/mri
> >
> > mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
> > -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
> >
> > logging cutting plane coordinates to ../scripts/ponscc.cut.log...
> >
> > INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
> >
> > using segmentation aseg.auto_noCCseg.mgz...
> >
> > reading input volume...done.
> >
> > searching for cutting planes...voxel to talairach voxel transform
> >
> > 0.964  -0.026  -0.002   8.591;
> >
> > 0.022   1.002   0.185  -15.064;
> >
> > -0.012  -0.183   0.940   20.634;
> >
> > 0.000   0.000   0.000   1.000;
> >
> > voxel to talairach voxel transform
> >
> > 0.964  -0.026  -0.002   8.591;
> >
> > 0.022   1.002   0.185  -15.064;
> >
> > -0.012  -0.183   0.940   2

[Freesurfer] problem with left/right parallelization

[Krieger, Donald N.]

I have successful runs of recon-all -autorecon1 and recon-all 
-autorecon2-volonly per your suggested sequence:
recon-all -s subj -autorecon1
recon-all -s subj -autorecon2-volonly
recon-all -s subj -autorecon2-perhemi -hemi rh -log recon-all-hemi rh.log 
-notify rh-done.log -openmp 4 &
recon-all -s subj -autorecon2-perhemi -hemi lh -log recon-all-hemi-lh.log 
-notify lh-done.log -openmp 4 &
while (rh-done.log AND lh-done.log do not both exist)
do
   sleep 1
end loop
recon-all -s -autorecon3

However my 2 runs of recon-all -autorecon2-perhemi are ending with no errors 
but after just a few seconds.
Is this correct?
Are there other functions which should be getting executed?
???

Here is one of the 2 recon-all commands.  The 2 log files are attached.
  recon-all   \
-s ${SubNo} \
-autorecon2-perhemi  \
-hemi rh   \
-log ${WD}/${SubNo}/recon-all-hemi_rh.log  \
-notify ${WD}/${SubNo}/rh-done.log  \
-openmp ${nCpus}   \
-no-isrunning   \

&


Thanks,

Don


Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh



recon-all-hemi_lh.log
Description: recon-all-hemi_lh.log


recon-all-hemi_rh.log
Description: recon-all-hemi_rh.log
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Re: [Freesurfer] -openmp 8 and -use-gpu questions

[Krieger, Donald N.]

Thanks very much for getting back so quickly.
The processing times were 5-6 hours for all instances.
There is an incremental but only modest improvement for 4/6 vs 8/12 processors.
I'll put up more information on the list when I've finished thinking this 
through.

Regards,
 
Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of zkauf...@nmr.mgh.harvard.edu
> Sent: Friday, May 01, 2015 1:41 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] -openmp 8 and -use-gpu questions
> 
> > I'm testing the total processing time of recon-all -all using -openmp
> > 4,6,8,12 .
> > The runs with 4 and 6 threads took almost the same amount of time.
> > The runs with 8 and 12 threads took almost the same amount of time.
> >
> > (1)Is the work divided evenly between the threads (mri_ca_register,
> > mri_en_register)?   Or is 4 or 8 preferred and 6 and 12 don't buy you
> > anything?
> 
> 
> I can verify that the gain in processing time due to additional threads falls 
> off
> rapidly with very little gain after 4. I dont know the exact times you got 
> from
> your tests, and I havent done a time analysis in awhile, but we've never 
> noticed
> a correlation preferring 4 and 8 threads over 6 and 12. However its an
> interesting result and could very well be the case.
> 
> 
> > (2)Is there a sync point in the software so that all the "other"
> > threads wait for the slowest one to complete.
> 
> 
> I dont do much of the openmp programming within freesurfer (only for
> debugging purposes) but as far as I can tell all the openmp relevant code 
> blocks
> occur at for-loop where threads are all created and diverge simultaneously and
> then sync and at the same time at the conclusion of the for-loop.
> 
> If you have an 8-12 processor machine and are looking to reduce your runtimes
> you can take advantage of the fact that the left and right hemispheres can be
> processed independently during the autorecon2 stage.
> You could write a custom script along the lines of:
> 
>   recon-all -s subj -autorecon1
>   recon-all -s subj -autorecon2-volonly
>   recon-all -s subj -autorecon2-perhemi -hemi rh -log recon-all-hemi rh.log -
> notify rh-done.log -openmp 4 &
>   recon-all -s subj -autorecon2-perhemi -hemi lh -log recon-all-hemi-lh.log -
> notify lh-done.log -openmp 4 &
>   while (rh-done.log AND lh-done.log do not both exist)
>   do
> sleep 1
>   end loop
>   recon-all -s -autorecon3
> 
> >
> > Also, I tried a run with -use-gpu.
> > I had to add a directory to LD_LIBRARY_PATH or I get an error on
> > failure to find one of the libcuda's That is now ok but I get the
> > following:
> >
> > Testing for CUDA device:
> > ERROR: Unable to acquire a CUDA device!
> > nvcc: NVIDIA (R) Cuda compiler driver
> > Copyright (c) 2005-2012 NVIDIA Corporation Built on
> > Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0,
> > V0.2.1221
> >
> > Acquiring CUDA device
> > Using default device
> > Linux comet-30-08.sdsc.edu 3.10.73-1.el6.elrepo.x86_64 #1 SMP Thu Mar
> > 26
> > 16:28:30 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux
> >
> > recon-all -s 173_1gpu exited with ERRORS at Thu Apr 30 09:17:42 PDT
> > 2015_PATH  but then I get the following error:
> >
> > Any thoughts would be welcome.
> >
> > Thanks,
> >
> 
> 
> Sorry but weve completely abandoned all support of CUDA in favor of openmp.
> That said, people successfully have and still do use cuda with freesurfer 
> v5.3.
> Assuming you have a cuda device compatible with the cuda libs shipped with
> freesurfer it should simply work without you having to modify
> LD_LIBRARY_PATH, but perhaps someone who has had success in this relm can
> chime in.
> 
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 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 . If the e-mail was sent to you in
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[Freesurfer] -openmp 8 and -use-gpu questions

[Krieger, Donald N.]

I'm testing the total processing time of recon-all -all using -openmp 4,6,8,12 .
The runs with 4 and 6 threads took almost the same amount of time.
The runs with 8 and 12 threads took almost the same amount of time.

(1)Is the work divided evenly between the threads (mri_ca_register, 
mri_en_register)?   Or is 4 or 8 preferred and 6 and 12 don't buy you anything?

(2)Is there a sync point in the software so that all the "other" threads 
wait for the slowest one to complete.

Also, I tried a run with -use-gpu.
I had to add a directory to LD_LIBRARY_PATH or I get an error on failure to 
find one of the libcuda's
That is now ok but I get the following:

Testing for CUDA device:
ERROR: Unable to acquire a CUDA device!
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_Sep_21_17:28:58_PDT_2012
Cuda compilation tools, release 5.0, V0.2.1221

Acquiring CUDA device
Using default device
Linux comet-30-08.sdsc.edu 3.10.73-1.el6.elrepo.x86_64 #1 SMP Thu Mar 26 
16:28:30 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 173_1gpu exited with ERRORS at Thu Apr 30 09:17:42 PDT 2015_PATH  
but then I get the following error:

Any thoughts would be welcome.

Thanks,

Don

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
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Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

[Krieger, Donald N.]

Dear Doug,

Thanks for getting back and for your patience.
I see.
mri_label2label does something much fancier and more precise than simply using 
a linear transformation to get from one to the other.
It definitely works as the transformed vectors of a label from several subjects 
plot right on top of those from fsaverage and, presumably, whatever target 
subject is specified.

Regards,
 
Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
> Sent: Friday, March 13, 2015 11:01 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors to
> talaraich
> 
> 
> 
> On 3/13/15 10:10 AM, Krieger, Donald N. wrote:
> > Dear List,
> >
> > Sorry to be unclear in my questions.  I had a fundamental misunderstanding
> which I hope to rectify.
> >
> > (1) It appears that what is called the "freesurfer" coordinate system
> (tkregister) is represented by subject fsaverage.  3D coordinate vectors in 
> label
> files generated for any subject's scan are in RAS coordinates in the fsaverage
> coordinate system.  Is this correct?
> No, they are in tkregister-coordinates in the individual's conformed 
> anatomical
> space (the coordinate system is defined by the way the col, row, and slice are
> converted into an XYZ)
> > (2) Under the assumption that (1) is true, I have plotted the vectors from 
> > label
> files (ROI: lh.postcentral) from fsaverage's and two subjects' scans on axial
> slices extracted from $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz .
> Since all three are in the same coordinate system, no transformation was
> needed.  The ROI for fsaverage's label file is plotted in black and appears to
> follow the gray/white boundary well.  The other 2 are plotted in red and green
> and are in the neighborhood but not the same.  Is this in line with what you
> would expect?
> This is probably not correct since the labels from individuals will need to be
> transformed. Try using mri_label2label
> 
> >
> > Regards,
> >
> > Don
> >
> >
> > Don Krieger, Ph.D.
> > Department of Neurological Surgery
> > University of Pittsburgh
> >
> >> -Original Message-
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> >> Sent: Thursday, March 12, 2015 4:25 PM
> >> To: freesurfer@nmr.mgh.harvard.edu
> >> Subject: Re: [Freesurfer] follow up and double check: transform RAS
> >> vectors to talaraich
> >>
> >> sorry, I don't know what you've done or what you are trying to do or
> >> what the mri_info command is related to. Can you fill in the details?
> >>
> >> On 03/12/2015 04:20 PM, Krieger, Donald N. wrote:
> >>> Do the results in the attached images make sense?
> >>> Does it make sense that the transformation was obtained: mri_info
> >>> --vox2ras-
> >> fls ?
> >>> Regards,
> >>>
> >>> Don
> >>>
> >>>
> >>> Don Krieger, Ph.D.
> >>> Department of Neurological Surgery
> >>> University of Pittsburgh
> >>>
> >>>
> >>>> -Original Message-
> >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >>>> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> >>>> Sent: Thursday, March 12, 2015 3:44 PM
> >>>> To: freesurfer@nmr.mgh.harvard.edu
> >>>> Subject: Re: [Freesurfer] follow up and double check: transform RAS
> >>>> vectors to talaraich
> >>>>
> >>>> what do you want us to check?
> >>>>
> >>>> On 03/12/2015 03:27 PM, Krieger, Donald N. wrote:
> >>>>> Dear List,
> >>>>>
> >>>>> I've done a couple of spot checks which appear to work but want to
> >>>>> double check with you.
> >>>>>
> >>>>> Attached are 5 axial cuts from fsaverage's orig.mgz 5 mm apart.
> >>>>>
> >>>>> The "white" surface vectors are shown in black for lh.postcentral.
> >>>>>
> >>>>> I also put all of the CC vectors from the aseg; these show on the
> >>>>> lower 3 cuts.
> >>>>>
> >>&g

Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

[Krieger, Donald N.]

Dear List,

Sorry to be unclear in my questions.  I had a fundamental misunderstanding 
which I hope to rectify.

(1) It appears that what is called the "freesurfer" coordinate system 
(tkregister) is represented by subject fsaverage.  3D coordinate vectors in 
label files generated for any subject's scan are in RAS coordinates in the 
fsaverage coordinate system.  Is this correct?
(2) Under the assumption that (1) is true, I have plotted the vectors from 
label files (ROI: lh.postcentral) from fsaverage's and two subjects' scans on 
axial slices extracted from $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz .  
Since all three are in the same coordinate system, no transformation was 
needed.  The ROI for fsaverage's label file is plotted in black and appears to 
follow the gray/white boundary well.  The other 2 are plotted in red and green 
and are in the neighborhood but not the same.  Is this in line with what you 
would expect?  

Regards,
 
Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, March 12, 2015 4:25 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors to
> talaraich
> 
> sorry, I don't know what you've done or what you are trying to do or what the
> mri_info command is related to. Can you fill in the details?
> 
> On 03/12/2015 04:20 PM, Krieger, Donald N. wrote:
> > Do the results in the attached images make sense?
> > Does it make sense that the transformation was obtained: mri_info --vox2ras-
> fls ?
> >
> > Regards,
> >
> > Don
> >
> >
> > Don Krieger, Ph.D.
> > Department of Neurological Surgery
> > University of Pittsburgh
> >
> >
> >> -Original Message-
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> >> Sent: Thursday, March 12, 2015 3:44 PM
> >> To: freesurfer@nmr.mgh.harvard.edu
> >> Subject: Re: [Freesurfer] follow up and double check: transform RAS
> >> vectors to talaraich
> >>
> >> what do you want us to check?
> >>
> >> On 03/12/2015 03:27 PM, Krieger, Donald N. wrote:
> >>> Dear List,
> >>>
> >>> I've done a couple of spot checks which appear to work but want to
> >>> double check with you.
> >>>
> >>> Attached are 5 axial cuts from fsaverage's orig.mgz 5 mm apart.
> >>>
> >>> The "white" surface vectors are shown in black for lh.postcentral.
> >>>
> >>> I also put all of the CC vectors from the aseg; these show on the
> >>> lower 3 cuts.
> >>>
> >>> I've also put in red and green the lh.postcentral "white" surface
> >>> vectors from two of my scans.
> >>>
> >>> What do you think?
> >>>
> >>> Regards,
> >>>
> >>> Don
> >>>
> >>> Signature0001
> >>>
> >>> Don Krieger, Ph.D.
> >>>
> >>> Department of Neurological Surgery
> >>>
> >>> Universityof Pittsburgh
> >>>
> >>> (412)648-9654 Office
> >>>
> >>> (412)521-4431 Cell/Text
> >>>
> >>>
> >>>
> >>> ___
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> gr...@nmr.mgh.harvard.edu
> >> Phone Number: 617-724-2358
> >> Fax: 617-726-7422
> >>
> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >> Outgoing:
> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> 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
> >> 

Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

[Krieger, Donald N.]

Do the results in the attached images make sense?
Does it make sense that the transformation was obtained: mri_info --vox2ras-fls 
?

Regards,
 
Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, March 12, 2015 3:44 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors to
> talaraich
> 
> what do you want us to check?
> 
> On 03/12/2015 03:27 PM, Krieger, Donald N. wrote:
> >
> > Dear List,
> >
> > I've done a couple of spot checks which appear to work but want to
> > double check with you.
> >
> > Attached are 5 axial cuts from fsaverage's orig.mgz 5 mm apart.
> >
> > The "white" surface vectors are shown in black for lh.postcentral.
> >
> > I also put all of the CC vectors from the aseg; these show on the
> > lower 3 cuts.
> >
> > I've also put in red and green the lh.postcentral "white" surface
> > vectors from two of my scans.
> >
> > What do you think?
> >
> > Regards,
> >
> > Don
> >
> > Signature0001
> >
> > Don Krieger, Ph.D.
> >
> > Department of Neurological Surgery
> >
> > Universityof Pittsburgh
> >
> > (412)648-9654 Office
> >
> > (412)521-4431 Cell/Text
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 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 . 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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Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

[Krieger, Donald N.]

I forget to include that the transform I used was obtained: mri_info aseg.mgz 
-vox2ras-fsl

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N.
Sent: Thursday, March 12, 2015 3:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] follow up and double check: transform RAS vectors to 
talaraich

Dear List,

I've done a couple of spot checks which appear to work but want to double check 
with you.
Attached are 5 axial cuts from fsaverage's orig.mgz 5 mm apart.
The "white" surface vectors are shown in black for lh.postcentral.
I also put all of the CC vectors from the aseg; these show on the lower 3 cuts.

I've also put in red and green the lh.postcentral "white" surface vectors from 
two of my scans.
What do you think?

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text

___
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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 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.

Re: [Freesurfer] newbie questions: transform RAS vectors to talaraich vectors and view

[Krieger, Donald N.]

Thanks for getting back so quickly and for the clear answers.
I was able to get the axial slices out by using mri_convert --split to create a 
.nii file.
ImageJ could read that in and reslice it.

Thanks again.

Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, March 12, 2015 11:27 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] newbie questions: transform RAS vectors to talaraich
> vectors and view
> 
> 
> On 03/12/2015 09:54 AM, Krieger, Donald N. wrote:
> >
> > Dear List,
> >
> > I have sets of vectors in RAS coordinates from many volunteers.
> >
> > I want to transform them into coordinates for a standard volume.
> >
> > (1) I presume the standard volume that makes sense to use is orig.mgz
> > in $FREESURFER_HOME/subjects/fsaverage/mri.  Please confirm.
> >
> Yes
> >
> > (2)I presume that I can transform the vectors contained in subject N's
> > .label files to talairaich coordinates using the transform in
> > $FREESURFER_HOME/subjects/subjectN/mri/transforms/talairach.xfm.
> > Please confirm.
> >
> Yes, though it is not easy to apply yourself. If you put the xyz into a label 
> file,
> then you can use mri_label2label. Note that the xyz have to be in an FS
> coordinate system. See
> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> >
> > (3)What tool can I use to convert orig.mgz into a sequence of axial
> > cuts in some standard graphics format, e.g. gif, png, tiff?
> >
> I don't know of one.
> >
> > Thanks and best regards,
> >
> > Don
> >
> > Signature0001
> >
> > Don Krieger, Ph.D.
> >
> > Department of Neurological Surgery
> >
> > Universityof Pittsburgh
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 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 . If the e-mail was sent to you in
> error but does not contain patient information, please contact the sender and
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[Freesurfer] newbie questions: transform RAS vectors to talaraich vectors and view

[Krieger, Donald N.]

Dear List,

I have sets of vectors in RAS coordinates from many volunteers.
I want to transform them into coordinates for a standard volume.

(1) I presume the standard volume that makes sense to use is orig.mgz in 
$FREESURFER_HOME/subjects/fsaverage/mri.  Please confirm.

(2)I presume that I can transform the vectors contained in subject N's 
.label files to talairaich coordinates using the transform in 
$FREESURFER_HOME/subjects/subjectN/mri/transforms/talairach.xfm.  Please 
confirm.

(3)What tool can I use to convert orig.mgz into a sequence of axial cuts in 
some standard graphics format, e.g. gif, png, tiff?

Thanks and best regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
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Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

[Krieger, Donald N.]

Glad it helped, Zack.
It’s such a pleasure to come across something I understand.

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Zachary Greenberg
Sent: Wednesday, March 04, 2015 7:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

awesome! thanks a bunch Don.


-zack

On Wed, Mar 4, 2015 at 4:24 PM, Krieger, Donald N. 
mailto:krieg...@upmc.edu>> wrote:
Hi Zack,

It looks like mris_info send that matrix out on the error output rather than 
the standard output.
I just tried it and you can get it by redirecting both to your file like this:
Try  mris_info lh.pial >& lh_info.txt

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 On Behalf Of Zachary Greenberg
Sent: Wednesday, March 04, 2015 7:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

Thanks bruce. It will work out fine if I can just pull out that c_(ras) array 
in a pipelined way to apply it to the ascii data.

I'm struggling a bit to achieve that though. I think because mris_info outputs 
the tables of *_(ras) info in a strange way. For example, if I try to cat the 
output of mris_info to a txt file: 'mris_info lh.pial > lh_info.txt', the text 
file will contain everything except the *_(ras) info table that you see if you 
just call the command by itself:


volume geometry:

extent  : (256, 256, 256)

voxel   : ( 1.,  1.,  1.)

x_(ras) : (-1.,  0.,  0.)

y_(ras) : ( 0.,  0., -1.)

z_(ras) : ( 0.,  1.,  0.)

c_(ras) : (-1.6000, -5.1750, -15.3313)

file: ../mri/filled-pretess255.mgz



Are there any mris_info experts on the team who might know how to circumvent 
this?



thanks again for your help!

-zack

On Wed, Mar 4, 2015 at 2:54 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Zack

the ascii format I don't think supports the c_ras info, which is why you see a 
shift

cheers
Bruce

On Wed, 4 Mar 2015, Zachary Greenberg wrote:
Ok I figured out that this shift corresponds to the c_(RAS) value in the
header of lh.pial, which you can get with 'mris_info lh.pial'
Alternatively you can get the first coordinate and subtract it from the
first coordinate of lh.pial.asc with 'mris_info lh.pial --v 0'

Is there a way I'm not thinking of to output c_(RAS) directly using
mris_info or a bash command (cat grep)?

Thanks again,

-zack

On Wed, Mar 4, 2015 at 12:54 PM, Zachary Greenberg
mailto:zacharyigreenb...@gmail.com>> wrote:
  Hi all,
I discovered that converting the mesh data from freesurfer lh.pial
format to ascii (.asc) causes a shift in the coordinates of the mesh.
You can see this by overlaying the two surfaces in freeview, and
looking at the difference between the [0 0 0] surface RAS coordinate
in lh.pial vs lh.pial.asc.

The shift is not consistent across different subjects. I'm wondering
if there is a way to fix this, or if there is some regularity in the
coordinate shift that can be used to correct (that I'm not seeing).

For example the difference coordinates between lh.pial and lh.pial.asc
in two different subjects are:
[  1.6 ,   5.18,  15.33]
[2.02, -15.80, 0.18]


Thanks for any help you can offer!

-zack








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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



--
Zachary Greenberg
Imaging Specialist
Department of Neurological Surgery
University of California, San Francisco
Email: 
Zachary<mailto:zigreen...@gmail.com>.greenb...@ucsf.edu<mailto:reenb...@memory.ucsf.edu>



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Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

[Krieger, Donald N.]

Hi Zack,

It looks like mris_info send that matrix out on the error output rather than 
the standard output.
I just tried it and you can get it by redirecting both to your file like this:
Try  mris_info lh.pial >& lh_info.txt

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Zachary Greenberg
Sent: Wednesday, March 04, 2015 7:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift

Thanks bruce. It will work out fine if I can just pull out that c_(ras) array 
in a pipelined way to apply it to the ascii data.

I'm struggling a bit to achieve that though. I think because mris_info outputs 
the tables of *_(ras) info in a strange way. For example, if I try to cat the 
output of mris_info to a txt file: 'mris_info lh.pial > lh_info.txt', the text 
file will contain everything except the *_(ras) info table that you see if you 
just call the command by itself:


volume geometry:

extent  : (256, 256, 256)

voxel   : ( 1.,  1.,  1.)

x_(ras) : (-1.,  0.,  0.)

y_(ras) : ( 0.,  0., -1.)

z_(ras) : ( 0.,  1.,  0.)

c_(ras) : (-1.6000, -5.1750, -15.3313)

file: ../mri/filled-pretess255.mgz



Are there any mris_info experts on the team who might know how to circumvent 
this?



thanks again for your help!

-zack

On Wed, Mar 4, 2015 at 2:54 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Zack

the ascii format I don't think supports the c_ras info, which is why you see a 
shift

cheers
Bruce

On Wed, 4 Mar 2015, Zachary Greenberg wrote:
Ok I figured out that this shift corresponds to the c_(RAS) value in the
header of lh.pial, which you can get with 'mris_info lh.pial'
Alternatively you can get the first coordinate and subtract it from the
first coordinate of lh.pial.asc with 'mris_info lh.pial --v 0'

Is there a way I'm not thinking of to output c_(RAS) directly using
mris_info or a bash command (cat grep)?

Thanks again,

-zack

On Wed, Mar 4, 2015 at 12:54 PM, Zachary Greenberg
mailto:zacharyigreenb...@gmail.com>> wrote:
  Hi all,
I discovered that converting the mesh data from freesurfer lh.pial
format to ascii (.asc) causes a shift in the coordinates of the mesh.
You can see this by overlaying the two surfaces in freeview, and
looking at the difference between the [0 0 0] surface RAS coordinate
in lh.pial vs lh.pial.asc.

The shift is not consistent across different subjects. I'm wondering
if there is a way to fix this, or if there is some regularity in the
coordinate shift that can be used to correct (that I'm not seeing).

For example the difference coordinates between lh.pial and lh.pial.asc
in two different subjects are:
[  1.6 ,   5.18,  15.33]
[2.02, -15.80, 0.18]


Thanks for any help you can offer!

-zack









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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 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.



--
Zachary Greenberg
Imaging Specialist
Department of Neurological Surgery
University of California, San Francisco
Email: 
Zachary.greenb...@ucsf.edu


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Longitudinal post processing

[Krieger, Donald N.]

Your environmental variables need to be set in the environment you use.
I don’t think the environment gets carried through when you use “sudo”.
That’s why your status messages show things like:

   Working in SUBJECTS_DIR: /analise//
$SUBJECTS_DIR didn’t get interpreted.

You can double check by trying: sudo printenv
which will give you a list of your environmental variables.

You probably can get it to work with something like:
   sudo ( source Script_With_EnvironmentalVariableSettings; long_mris_slopes 
--qdec $SUBJECTS_DIR/qdec … )
or even
   sudo   ( export FREESURFER_HOME=/ABC/DEF ; export 
SUBJECTS_DIR=${FREESURFER_HOME/subjects ; long_mris_slopes --qdec 
$SUBJECTS_DIR/qdec … )

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of carolina.mr
Sent: Tuesday, February 24, 2015 5:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal post processing

Hello,

I am trying to make the Two Stage Longitudinal processing and when I give the 
command to prepare the data with QCACHE.

I've already set up the environment for FREESURFER_HOME, but it keeps appearing 
the error message:

ERROR: FREESURFER_HOME not defined in environment

ERROR 1 : mri_label2label mapping the label failed?





Following, there is a copy of my command and the error messages that appeared.


sudo long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.qdec.table.dat 
--meas thickness --hemi lh \ --do-avg --do-rate --do-pc1 --do-spc --do-stack 
--do-label \ --time years --qcache $SUBJECTS_DIR/fsaverage/ --sd $SUBJECTS_DIR/

Password:

Parsing the qdec table: /analise//qdec/longRRMSP01.qdec.table.dat



Working in SUBJECTS_DIR: /analise//





Working on hemi: lh





Subject-Template: P01_TP





INFO: 2 TPs in P01_TP , mean age: 2.25





===

SUBJECT P01_TP  Intersecting Within-Subject Cortex Label



cp /analise//P01_RM1.long.P01_TP/label/lh.cortex.label 
/analise//P01_TP/label/lh.long.cortex.label







mris_label_calc intersect /analise//P01_RM2.long.P01_TP/label/lh.cortex.label 
/analise//P01_TP/label/lh.long.cortex.label 
/analise//P01_TP/label/lh.long.cortex.label









===

SUBJECT P01_TP  mapping label to QCache



mri_label2label --srclabel /analise//P01_TP/label/lh.long.cortex.label 
--srcsubject P01_TP --trglabel 
/analise//P01_TP/label/lh.long.cortex./analise//fsaverage/.label --trgsubject 
/analise//fsaverage/ --regmethod surface --hemi lh





srclabel = /analise//P01_TP/label/lh.long.cortex.label

srcsubject = P01_TP

trgsubject = /analise//fsaverage/

trglabel = /analise//P01_TP/label/lh.long.cortex./analise//fsaverage/.label

regmethod = surface



srchemi = lh

trghemi = lh

trgsurface = white

srcsurfreg = sphere.reg

trgsurfreg = sphere.reg

usehash = 1

Use ProjAbs  = 0, 0

Use ProjFrac = 0, 0

DoPaint 0



ERROR: FREESURFER_HOME not defined in environment

ERROR 1 : mri_label2label mapping the label failed?





Thank you, Carolina
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Re: [Freesurfer] time critical problem: mri_ca_register failure during recon-all run

[Krieger, Donald N.]

Thanks again, Bruce.
The time problem precludes running with a single cpu.
But you jogged my memory and I was fooling around with freeview while recon-all 
was running.
I might have overrun the memory with it as I was loading 10's of 1000's of 
points to plot which really pushes it.
I'll try with 5 cpus again since my time is so short and leave the machine idle 
otherwise.

Regards,
 
Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, February 11, 2015 9:53 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] time critical problem: mri_ca_register failure 
> during
> recon-all run
> 
> Hi Don
> 
> does it repeatably die in the same place when you run it with openmp 5? Are
> you sure nothing else was running at the time? Try running it with openmp 1
> and make sure nothing else is running and see if it finishes sorry, not sure 
> what
> else to suggest. If it dies in the same spot, upload the entire subject dir 
> and let
> us know
> 
> good luck
> Bruce
> 
> 
> On
> Wed, 11 Feb 2015, Krieger, Donald N. wrote:
> 
> > Thanks for responding so quickly, Bruce.
> > Yes I was running a single job on the 6-core machine and have used it and
> this version of recon-all successfully before.
> > The freesurfer instance was downloaded a few weeks ago - it is the Centos6
> one.
> > I don't know how to tell which version of the entire package it is.
> > recon-all -version returns:
> >  $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
> > mri_ca_register -version returns:
> >  stable5
> > nu_estimate_np_and_em -version returns:
> >   Package MNI N3, version 1.10, compiled by nicks@minerva
> > (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 preceded by a bunch
> of deprecation notices.
> >
> > ???
> >
> > Regards,
> >
> > Don
> >
> >
> > Don Krieger, Ph.D.
> > Department of Neurological Surgery
> > University of Pittsburgh
> > (412)648-9654 Office
> > (412)521-4431 Cell/Text
> >
> >
> >> -Original Message-
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> >> Sent: Wednesday, February 11, 2015 9:39 AM
> >> To: Freesurfer support list
> >> Subject: Re: [Freesurfer] time critical problem: mri_ca_register
> >> failure during recon-all run
> >>
> >> Hi Don
> >>
> >> are you running a single job on the 8G machine? What FS version? We
> >> haven't seen any core dumps in mri_ca_register recently. If you run
> >> it without openmp does it work? Kind of worrisome that it dies in a
> >> different place on a different machine Bruce
> >>
> >>
> >> On Wed, 11 Feb 2015, Krieger, Donald N. wrote:
> >>
> >>>
> >>> Dear list:
> >>>
> >>>
> >>>
> >>> We are under a significant deadline on which this freesurfer run depends.
> >>>
> >>> I’m reposting from last night along with a bit of additional information.
> >>>
> >>> A 2nd run on a different box yielded:
> >>>
> >>>    nu_correct: crashed while running nu_estimate_np_and_em
> >>> (termination
> >>> status=256)
> >>>
> >>>
> >>> Also, the box on which the run detailed below was done has 8 GBytes
> >>> of RAM, not 8 Mbytes – sorry about that.
> >>>
> >>>
> >>>
> >>> Any help and direction you can provide with this error would be
> appreciated.
> >>>
> >>> The full log is attached.
> >>>
> >>> I was running with –openmp 5 on a machine with 6 cores and 8 Mbytes
> >>> of
> >> RAM.
> >>>
> >>>
> >>>
> >>> 0033: dt=73.984000, rms=0.641 (0.133%), neg=0, invalid=96777
> >>>
> >>> 0034: dt=73.984000, rms=0.640 (0.104%), neg=0, invalid=96777
> >>>
> >>> 0035: dt=73.984000, rms=0.640 (0.095%), neg=0, invalid=96777
> >>>
> >>> 0036: dt=517.888000, rms=0.639 (0.162%), neg=0, invalid=96777
> >>>
> >>> 0037: dt=23.12, rms=0.639 (-0.002%), neg=0, invalid=96777
> >>>
> >>> blurring input image with Gaussian with sigma=0.500...
> >>>
> >>> :

Re: [Freesurfer] time critical problem: mri_ca_register failure during recon-all run

[Krieger, Donald N.]

Thanks for responding so quickly, Bruce.
Yes I was running a single job on the 6-core machine and have used it and this 
version of recon-all successfully before.
The freesurfer instance was downloaded a few weeks ago - it is the Centos6 one.
I don't know how to tell which version of the entire package it is.
recon-all -version returns:
  $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
mri_ca_register -version returns:
  stable5
 nu_estimate_np_and_em -version returns:
   Package MNI N3, version 1.10, compiled by nicks@minerva 
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
 preceded by a bunch of deprecation notices.

???

Regards,
 
Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, February 11, 2015 9:39 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] time critical problem: mri_ca_register failure 
> during
> recon-all run
> 
> Hi Don
> 
> are you running a single job on the 8G machine? What FS version? We haven't
> seen any core dumps in mri_ca_register recently. If you run it without openmp
> does it work? Kind of worrisome that it dies in a different place on a 
> different
> machine Bruce
> 
> 
> On Wed, 11 Feb 2015, Krieger, Donald N. wrote:
> 
> >
> > Dear list:
> >
> >
> >
> > We are under a significant deadline on which this freesurfer run depends.
> >
> > I’m reposting from last night along with a bit of additional information.
> >
> > A 2nd run on a different box yielded:
> >
> >    nu_correct: crashed while running nu_estimate_np_and_em
> > (termination
> > status=256)
> >
> >
> > Also, the box on which the run detailed below was done has 8 GBytes of
> > RAM, not 8 Mbytes – sorry about that.
> >
> >
> >
> > Any help and direction you can provide with this error would be appreciated.
> >
> > The full log is attached.
> >
> > I was running with –openmp 5 on a machine with 6 cores and 8 Mbytes of
> RAM.
> >
> >
> >
> > 0033: dt=73.984000, rms=0.641 (0.133%), neg=0, invalid=96777
> >
> > 0034: dt=73.984000, rms=0.640 (0.104%), neg=0, invalid=96777
> >
> > 0035: dt=73.984000, rms=0.640 (0.095%), neg=0, invalid=96777
> >
> > 0036: dt=517.888000, rms=0.639 (0.162%), neg=0, invalid=96777
> >
> > 0037: dt=23.12, rms=0.639 (-0.002%), neg=0, invalid=96777
> >
> > blurring input image with Gaussian with sigma=0.500...
> >
> > : dt=0.000, rms=0.639, neg=0, invalid=96777
> >
> > 0038: dt=92.48, rms=0.638 (0.081%), neg=0, invalid=96777
> >
> > Segmentation fault (core dumped)
> >
> > ERROR: mri_ca_register with non-zero status 139
> >
> > but continuing despite the error
> >
> > #--
> >
> > #@# CA Reg Inv Tue Feb 10 19:24:19 EST 2015
> >
> > /home/kriegerd/Contrib/freesurfer/subjects/175/mri
> >
> >
> >
> > mri_ca_register -invert-and-save transforms/talairach.m3z
> >
> >
> >
> > Loading, Inverting, Saving, Exiting ...
> >
> > Reading transforms/talairach.m3z
> >
> > ERROR: cannot find or read transforms/talairach.m3z
> >
> > ERROR: mri_ca_register with non-zero status 0
> >
> > Linux OfficeFedora21 3.17.4-301.fc21.x86_64 #1 SMP Thu Nov 27 19:09:10
> > UTC
> > 2014 x86_64 x86_64 x86_64 GNU/Linux
> >
> >
> >
> > recon-all -s 175 exited with ERRORS at Tue Feb 10 19:24:19 EST 2015
> >
> >
> >
> > Regards,
> >
> >
> >
> > Don
> >
> >
> >
> > Signature0001
> >
> > Don Krieger, Ph.D.
> >
> > Department of Neurological Surgery
> >
> > University of Pittsburgh
> >
> >
> >
> >
> >

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[Freesurfer] time critical problem: mri_ca_register failure during recon-all run

[Krieger, Donald N.]

Dear list:

We are under a significant deadline on which this freesurfer run depends.
I'm reposting from last night along with a bit of additional information.
A 2nd run on a different box yielded:
   nu_correct: crashed while running nu_estimate_np_and_em (termination 
status=256)


Also, the box on which the run detailed below was done has 8 GBytes of RAM, not 
8 Mbytes - sorry about that.

Any help and direction you can provide with this error would be appreciated.
The full log is attached.
I was running with -openmp 5 on a machine with 6 cores and 8 Mbytes of RAM.

0033: dt=73.984000, rms=0.641 (0.133%), neg=0, invalid=96777
0034: dt=73.984000, rms=0.640 (0.104%), neg=0, invalid=96777
0035: dt=73.984000, rms=0.640 (0.095%), neg=0, invalid=96777
0036: dt=517.888000, rms=0.639 (0.162%), neg=0, invalid=96777
0037: dt=23.12, rms=0.639 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
: dt=0.000, rms=0.639, neg=0, invalid=96777
0038: dt=92.48, rms=0.638 (0.081%), neg=0, invalid=96777
Segmentation fault (core dumped)
ERROR: mri_ca_register with non-zero status 139
but continuing despite the error
#--
#@# CA Reg Inv Tue Feb 10 19:24:19 EST 2015
/home/kriegerd/Contrib/freesurfer/subjects/175/mri

mri_ca_register -invert-and-save transforms/talairach.m3z

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
Linux OfficeFedora21 3.17.4-301.fc21.x86_64 #1 SMP Thu Nov 27 19:09:10 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 175 exited with ERRORS at Tue Feb 10 19:24:19 EST 2015

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh



175_recon-all.log
Description: 175_recon-all.log
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[Freesurfer] mri_ca_register failure during recon-all run

[Krieger, Donald N.]

Any help and direction you can provide with this error would be appreciated.
The full log is attached.
I was running with -openmp 5 on a machine with 6 cores and 8 Mbytes of RAM.

0033: dt=73.984000, rms=0.641 (0.133%), neg=0, invalid=96777
0034: dt=73.984000, rms=0.640 (0.104%), neg=0, invalid=96777
0035: dt=73.984000, rms=0.640 (0.095%), neg=0, invalid=96777
0036: dt=517.888000, rms=0.639 (0.162%), neg=0, invalid=96777
0037: dt=23.12, rms=0.639 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
: dt=0.000, rms=0.639, neg=0, invalid=96777
0038: dt=92.48, rms=0.638 (0.081%), neg=0, invalid=96777
Segmentation fault (core dumped)
ERROR: mri_ca_register with non-zero status 139
but continuing despite the error
#--
#@# CA Reg Inv Tue Feb 10 19:24:19 EST 2015
/home/kriegerd/Contrib/freesurfer/subjects/175/mri

mri_ca_register -invert-and-save transforms/talairach.m3z

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
Linux OfficeFedora21 3.17.4-301.fc21.x86_64 #1 SMP Thu Nov 27 19:09:10 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 175 exited with ERRORS at Tue Feb 10 19:24:19 EST 2015

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh



175_recon-all.log
Description: 175_recon-all.log
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[Freesurfer] freeview shared library fault with fix after update to Fedora 21

[Krieger, Donald N.]

Dear freesurfer team:

I just updated to Fedora 21 and freeview failed with errors finding 
libpng12.so.0 and libXss.so.1 .
I copied these from an earlier version of Fedora into /usr/lib64 and freeview 
now works.

I'm running recon-all under this new release and will post back if there are 
problems.
The linux version is 3.17.4-301.fc21.x86_64 #1 SMP .

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text

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Re: [Freesurfer] Freesurfer Digest, Vol 131, Issue 28

[Krieger, Donald N.]

Muhammad,

I think your question is not so much a freesurfer one but more general.
You want to run 40 jobs in the background so terminals won't be needed once 
they are spawned.

The way to do it is issue commands like this:
( cmds for job1; cmds for job2; ... ; cmds for jobM ) &
( cmds for jobM+1; ... ; cmds for job2M ) &

The & places each group of M commands in the background.
The M jobs will run one after the other.
Once you've issued these commands, you probably can simply exit from your 
terminal and they will continue to run.

For freesurfer, I suggest using -openmp 6  to provide access to multiple cores 
to each job so they complete faster.  With -openmp 6 and 40 cores, I would 
stick with no more than 10 simultaneously running jobs.

Hopefully this is helpful.

Don

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Muhammad Naveed Iqbal 
Qureshi [mniqure...@hotmail.com]
Sent: Tuesday, January 20, 2015 8:28 PM
To: Freesurfer maillist; fis...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 131, Issue 28

 Hi Bruce,

I tried it for 40 subjects for first time yesterday, but eventually 28 
terminals were self killed and only 12 subjects were processed successfully.
Can you guide me why did it happen.
My machine has 40 CPU cores with 256GB ram.

Secondly how can I preprocess the incomplete subjects?

Thank you.


Best Regards,
Muhammad Naveed Iqbal Qureshi
P please don't print this e-mail unless you really need to


> From: freesurfer-requ...@nmr.mgh.harvard.edu
> Subject: Freesurfer Digest, Vol 131, Issue 28
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Tue, 20 Jan 2015 12:00:02 -0500
>
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. regarding license.txt file (Kanel, Prabesh)
> 2. Re: regarding license.txt file (zkauf...@nmr.mgh.harvard.edu)
> 3. converting .nii to .mgz (Borzello, Mia)
> 4. using merge_stats_tables to merge broadman areas for multiple
> subjects. (Salil Soman)
> 5. Re: converting .nii to .mgz (Bruce Fischl)
> 6. Re: converting .nii to .mgz (Borzello, Mia)
> 7. recon-all on group (Muhammad Naveed Iqbal Qureshi)
> 8. standardized community affiliation vector (Alexander Lebedev)
> 9. Re: Viewing QDEC results in tksurfer (Worker, Amanda)
> 10. mri_convert crash after updating with tracula add update
> 2014/05/26 on Ubuntu 14.04 lts (Knut J Bjuland)
> 11. Re: converting .nii to .mgz (Bruce Fischl)
> 12. Re: recon-all on group (Bruce Fischl)
> 13. Re: Viewing QDEC results in tksurfer (Bruce Fischl)
> 14. Re: Viewing QDEC results in tksurfer (Worker, Amanda)
> 15. Re: converting .nii to .mgz (Douglas N Greve)
> 16. Re: Viewing QDEC results in tksurfer (Douglas N Greve)
> 17. Re: Contrast files for a complex ANCOVA (involving multiple
> categorical covariates) model (Douglas N Greve)
> 18. Re: converting .nii to .mgz (Borzello, Mia)
> 19. Re: converting .nii to .mgz (mborze...@partners.org)
> 20. Re: converting .nii to .mgz (Azeez Adebimpe)
> 21. Re: converting .nii to .mgz (Douglas N Greve)
>
>
> --
>
> Message: 1
> Date: Mon, 19 Jan 2015 21:50:51 +
> From: "Kanel, Prabesh" 
> Subject: [Freesurfer] regarding license.txt file
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Message-ID:
> 
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I downloaded the latest version of the freesurfer and tried to install it. 
> After running the installation, I registered my information in 
> https://surfer.nmr.mgh.harvard.edu/registration.html
>
> I received an email after few minutes with an information that I have to 
> replace a text inside the license.txt file. So, I went back and try to do 
> that. But I cannot locate the license.txt file. It does contain LICENSE file 
> but doesn't have an information that I need to replace.
>
> Later, I went back and download the latest version of freesurfer again 
> thinking I may have made a mistake at first installation but even the later 
> installation didn't contain any license.txt file.
>
> The freesurfer that I download was from 
> https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#Download
>
> The detail of the file is below
> Linux
>
> CentOS 6 x86_64 (64b)
>
> stable v5.3.0
>
> 15 May 2013
>
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

Re: [Freesurfer] recon-all error

[Krieger, Donald N.]

It looks like there's a typo in your recon-all command - there's a space 
between "-"  and autorecon3 .

Regards,
 
Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia
> Sent: Friday, January 09, 2015 5:30 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
> 
> Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects.
> I attached the output error for recon-all.
> 
> Thanks,
> m
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
> boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, January 08, 2015 4:27 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error
> 
> did you look in
> 
> /autofs/space/huygens_001/users/mia/subjects
> 
> Can you send us the screen output of recon-all?
> 
> On Thu, 8 Jan 2015, Borzello,
> Mia wrote:
> 
> > I looked for that file and did not see a BI22_SurferOutput folder at all.
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> > [fis...@nmr.mgh.harvard.edu]
> > Sent: Thursday, January 08, 2015 2:34 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] recon-all error
> >
> > Hi Mia
> >
> > can you send us the recon-all.log? I don't think you included the
> > error message in your email so there isn't much for us to go on.
> >
> > thanks
> > Bruce
> >
> > On Thu, 8 Jan 2015, Borzello, Mia wrote:
> >
> >>
> >> Hi Freesurfers,
> >>
> >> I'm wondering if you can help with the following error that occurred
> >> when trying to create a reconstruction:
> >>
> >> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
> >>
> >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
> >>
> >> RedHat release: CentOS release 6.5 (Final)
> >>
> >> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
> >>
> >> NMR Center info (/space/freesurfer exists):
> >>
> >>   machine: huygens
> >>
> >>   SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
> >>
> >>   PWD: /autofs/space/huygens_001/users/mia/subjects
> >>
> >>   ssh huygens
> >>   setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
> >>   cd /autofs/space/huygens_001/users/mia/subjects
> >>
> >>
> >> 1)BI22
> >> 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject
> >> BI22_SurferOutput
> >> -
> i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_B
> >> I19/4571
> >> /4571157.dcm
> >> 3)recon-all -s  exited with ERRORS at Thu Jan  8 13:08:33 EST 2015
> >>
> >>
> >> Thanks,
> >> m
> >>
> >>
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
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> >
> >
> >
> ___
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] From bedpostX and recon-all to tracula

[Krieger, Donald N.]

It looks like the ln -s command is failing either because dwi.nii.gz does not 
exist or data.nii.gz does exist.
I think you've ruled out that you don't have write permission to the directory 
by trying to execute it as root.

ln -sf /media/Sokol/Subj/041/dmri/dwi.nii.gz 
/media/Sokol/Subj/041/dmri/data.nii.gz


Don

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Watson, Christopher 
[christopher.wat...@childrens.harvard.edu]
Sent: Monday, December 15, 2014 8:42 PM
To: Freesurfer support list; Anastasia  Yendiki
Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula

I think certain filesystems don't support sym linking (e.g. FAT32). So that 
might be it.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme 
[katherine.da...@gmail.com]
Sent: Monday, December 15, 2014 5:29 PM
To: Anastasia Yendiki
Cc: Freesurfer support list
Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula

After removing this I have a new (possibly unrelated error):
mv -f /media/Sokol/Subj/041/dmri/bvecs /media/Sokol/Subj/041/dmri/bvecs.norot
xfmrot /media/Sokol/Subj/041/dmri/dwi.ecclog 
/media/Sokol/Subj/041/dmri/bvecs.norot /media/Sokol/Subj/041/dmri/bvecs
ln -sf /media/Sokol/Subj/041/dmri/dwi.nii.gz 
/media/Sokol/Subj/041/dmri/data.nii.gz
ln: creating symbolic link `/media/Sokol/Subj/041/dmri/data.nii.gz': Operation 
not permitted

This persists even when I run the command as the root user and regardless of 
the permissions settings of the folder and the fdwi.nii.gz file.

Any ideas?

On Mon, Dec 15, 2014 at 3:07 PM, Anastasia Yendiki 
mailto:ayend...@nmr.mgh.harvard.edu>> wrote:

It's hard to tell what's causing the error without seeing the entire 
trac-all.log. However, by glancing at your config file you seem to still have 
B0 inhomogeneity correction turned on (dob0 = 1) but without specifying any 
field map dicoms. I'd turn it off and see if that fixes it.


On Mon, 15 Dec 2014, Katherine Damme wrote:

Where would I be specifying a directory as an input/output?

I used the following cmd: /usr/local/freesurfer/bin/trac-all -prep -c dmri.fy

On Sun, Dec 14, 2014 at 7:12 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
  Hi Katerine

  the COR-* format is an old one that we don't use anymore. If you specify 
a directory as an
  input/output we will assume that it contains COR files, which is probably 
what you are seeing.

  cheers
  Bruce


  On Sun, 14 Dec 2014, Katherine Damme wrote:

At what point is the COR-*.info file made?
I got the following error:

corRead(): can't open file /media/Sokol/Subj/COR-.info
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/Sokol/Subj/...
Linux 
kate.ad.wcas.northwestern.edu 
2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec
13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 12 12:54:40 CST 2014

[ksd770@kate 041]# ls /media/Sokol/Subj/COR-*

On Thu, Dec 11, 2014 at 2:48 PM, Anastasia Yendiki
mailto:ayend...@nmr.mgh.harvard.edu>> 
wrote:

  No, those are field maps used to correct for inhomogeneities 
in
  the main magnetic field (which in MRI lingo is referred to as
  the B0 field, not to be confused with the b=0 images). You can
  skip that correction (you have to skip it if you don't have
  field maps).

  On Thu, 11 Dec 2014, Katherine Damme wrote:

I am sorry, I am a bit confused. What am I supposed
to be specifying under
the b0mlist and b0plist?

I thought that it was the B0 low-b image from
diffusion.

Thank you!

On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki

mailto:ayend...@nmr.mgh.harvard.edu>> wrote:

  Hi Kate - The screenshot looks more like a
low-b image from a
  diffusion scan than a field map. In case this
helps, the phase
  map data will have either 2 volumes (2 phase
maps acquired at
  different echo times) or 1 volume (the
difference of 2 such
  phase maps).

  Best,
  a.y

  

Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch

[Krieger, Donald N.]

Dear Jens,

I can offer just a bit of information and I also have a question.
We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos 6 
compiles work.
The package appears to be self-contained as I have seen no faults on failures 
to find shared libraries.
We simply untar freesurfer to a convenient location and set the PATH and 
FREESURFERHOME environment variables accordingly.
I see no reason why that shouldn't work in a cloud solution except that I do 
not know what you have in mind as a use for your solution.
Will there be a group of users who are provided access so that they can run 
freesurfer on an image data set through a portal to your cloud?
Are you using the cloud to distribute the calculation to many machines?
If so, what is the "granularity" of this, e.g. does one freesurfer run get one 
machine?

Regards,
 
Don
 

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Jens Offenbach
> Sent: Wednesday, November 19, 2014 5:47 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-
> patch
> 
> We are currently working on a solution that brings FreeSurfer in the cloud.
> Unfortunately, we are facing a lot of problems. Hopefully, someone can help
> me:
> 
> I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to
> download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu family?
> 
> On the FTP server I have found a patch for 5.3.0, but I am not sure how to 
> apply
> it or if I must apply it? The Readme says to replace “mri_segstats”. What 
> about
> the other files “recon-all, fsfast, tksurferfv, …”?
> 
> I want to reduce the archive to its bare minimum, otherwise the automated
> deployment process takes too long. It should contain only those files which 
> are
> necessary to execute the pipeline without any viewer or examples. Which files
> and folders can be deleted safely?
> 
> The most important issue is to monitor the FreeSurfer pipeline execution. I 
> know
> that the scripts folder contains some status files which offer important data
> helping me to monitor the pipeline execution progress of “recon-all”.
> Unfortunately, that is not enough… If one step takes e.g. approximately 20
> hours, I have to say something about the progress within this current step. Is
> there any possibility to monitor the progress of a single step. We need
> something that allows us to say e.g. that Step “CA Reg” has 34 % of its work
> done so far which means that the overall pipeline progress is e.g. 63 %. Is it
> possible to say that a specific step takes a specific portion of the overall
> pipeline execution time. What influences this portion (format or quality of 
> input,
> platform, …)?
> 
> Thank you very much for your help!
> 
> Regards
> Jens
> 
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 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 . If the e-mail was sent to you in
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Re: [Freesurfer] freeview fault: PETSC Error ... PERSISTENT

[Krieger, Donald N.]

Hi Nick,



I downloaded the most recent version of freeview.bin using wget as you 
suggested and ran it on two different machines.

It appeared to load a volume file fully whereas before it was crashing when 
showing it had loaded only 1%.

But it still crashes after that with the message below my signature.



I tried a few different .mgz files including the original one with the same 
result.  Both the machines on which I ran it have 8 GBytes of RAM.  Any other 
thoughts would be welcome.



Regards,



Don



[0]PETSC ERROR: 


[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find m

emory corruption errors

[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run

[0]PETSC ERROR: to get more information on the crash.

[0]PETSC ERROR: - Error Message 


[0]PETSC ERROR: Signal received!

[0]PETSC ERROR: 


[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124

[0]PETSC ERROR: See docs/changes/index.html for recent updates.

[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.

[0]PETSC ERROR: See docs/index.html for manual pages.

[0]PETSC ERROR: 


[0]PETSC ERROR: Unknown Name on a linux-gnu named donHome1TB by kriegerd Mon 
Nov 10 13:48:15 2014

[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt

[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010

[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-sha

red=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3

[0]PETSC ERROR: 


[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file

[unset]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0







> -Original Message-

> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-

> boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH

> Sent: Tuesday, November 04, 2014 11:59 PM

> To: Freesurfer support list

> Subject: Re: [Freesurfer] freeview fault: PETSC Error ...

>

> you can try downloading our nightly 'dev' build of freeview, from here:

>

> https://surfer.nmr.mgh.harvard.edu/fswiki/Download

>

> or here's a quicker way (this is a one-line command... wget ):

>

> wget

> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin>

> 86_64/freeview.bin<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin>

>

> and copy it to $FREESURFER_HOME/bin

> then

> chmod a+x $FREESURFER_HOME/bin/freeview.bin

>

> N.

>

>

> On Tue, 2014-11-04 at 12:35 +, Krieger, Donald N. wrote:

> > I recently downloaded and installed

> > freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz .

> >

> > I had been running this version previously but had to reload

> > everything due to a disk crash.

> >

> >

> >

> > recon-all –all goes to completion with no errors.

> >

> > freeview starts up fine but fails on loading a volume file with the

> > PETC error listed below.

> >

> > I found several references to this error in the archive but no

> > resolution for my problem.

> >

> > Any thoughts would be welcome – thanks.

> >

> >

> >

> > [0]PETSC ERROR:

> > --

> > --

> >

> > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,

> > probably memory access out of range

> >

> > [0]PETSC ERROR: Try option -start_in_debugger or

> > -on_error_attach_debugger

> >

> > [0]PETSC ERROR: or see

> > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.ht

> > ml#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man

> > libgmalloc on Apple to find memor

[Freesurfer] freeview fault: PETSC Error ...

[Krieger, Donald N.]

I recently downloaded and installed 
freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz .
I had been running this version previously but had to reload everything due to 
a disk crash.

recon-all -all goes to completion with no errors.
freeview starts up fine but fails on loading a volume file with the PETC error 
listed below.
I found several references to this error in the archive but no resolution for 
my problem.
Any thoughts would be welcome - thanks.

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named BTRC-Server01 by kriegerd Tue 
Nov  4 06:55:17 2014
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text

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Re: [Freesurfer] lh.BA.annot vs lh.BA.thresh.annot ... generalization question

[Krieger, Donald N.]

Thanks for getting back, Bruce.

Regards,
 
Don
 
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Thursday, September 11, 2014 8:26 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] lh.BA.annot vs lh.BA.thresh.annot ... generalization
> question
> 
> Hi Don
> 
> no, it doesn't make sense for the aparc since it is a complete tiling of the
> surface. Each point is assigned the most likely label with no holes, so no
> thresholding is needed.
> 
> cheers
> Bruce
> On Thu, 11 Sep 2014, Krieger, Donald N. wrote:
> 
> >
> > Hi Anastasia or anyone,
> >
> >
> >
> > Are there any other groups of labels which are, by default, produced
> > in comparable less vs more restrictive ways?
> >
> > For instance, is there a way to produce lh.aparc.thresh.annot with
> > comparably constrained labels?
> >
> > And does it make sense to do so?
> >
> >
> >
> > Regards,
> >
> >
> >
> > Don
> >
> >
> >
> > 
> >
> > >
> >
> > >
> >
> > > On 14-09-08 12:39 PM, Anastasia Yendiki wrote:
> >
> > > > Hi David - On the difference between .thresh and "not .thresh" labels:
> >
> > > > The BA labels come from averaging histologically derived labels
> > > > from
> >
> > > > a set of post mortem brains. The non-thresholded version is just
> > > > the
> >
> > > > sum of the corresponding labels from the different brains in
> >
> > > > fsaverage space. So vertices are included even if only one of the
> >
> > > > brains had their BA in that vertex, which means that these labels
> >
> > > > are going to be rather large. In the thresholded version, a
> >
> > > > threshold has been applied to the average BA label, to make it
> > > > have
> >
> > > > an area as close as possible to the average area of the individual
> > > > BA
> > labels. I hope this makes sense.
> >
> > > >
> >
> > > > a.y
> >
> > 
> >
> >
> >
> >
> >

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