[Freesurfer] volume to subcortical surfaces

[Peled, Noam]

Hello,
How can I get a fsfast contrast map projection on the subcortical surfaces? The 
sig.nii for each hemisphere has a value per vertex structure, but the mni305 
result is per voxel.
I used mri_vol2vol and mri_segstats to get statistics for each subcortical 
structure, but I need a value per vertex data. I can use the aseg.mgz as a 
mask, and get all the voxels per structure, but still I need to project it onto 
its surface.

Thanks,
Noam
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[Freesurfer] mri_pretess on fsaverage

[Peled, Noam]

Hello,
Is there a way to run mri_pretess on fsaverage? It has no mri/norm.mgz file.
I'm trying to create surface files for each subcortical structure using 
mri_pretess, mri_tessellate and mris_smooth.

Thanks!
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[Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation

[Peled, Noam]

Hey all,
I used mri_aparc2aseg to map the cortical labels from the laus250 parcellation.
Now I need to create a new lookup table, mainly for displaying the labels' 
names in freeview.
How can I know what id each label gets in my new laus+aseg.mgz file?

Thanks,
Noam 
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Re: [Freesurfer] lables id in a new aparc+aseg file, created from laus250 parcellation

[Peled, Noam]

Hey Bruce,
I meant for the Lausanne250 parcellation 
(http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048121)
The problem is with the #index column. To create a custom lookup table, I need 
to know what is the #index each label gets in the output file of
mri_aparc2aseg.
I want to users to be able to load this new mgz file into freeview with the 
right lookup table.

Thanks,
Noam


On Fri, 30 Oct 2015, Bruce wrote:

> what is the laus250 parcellation? The lookup tables are in text so you
> should be able to open one in an editor and see what the format is. It's
> pretty straightforward. # lines are comments, then it is

>  

> cheers
> Bruce


On Fri, 30 Oct 2015, Peled, Noam wrote:

> Hey all,
> I used mri_aparc2aseg to map the cortical labels from the laus250
> parcellation.
> Now I need to create a new lookup table, mainly for displaying the labels'
> names in freeview.
> How can I know what id each label gets in my new laus+aseg.mgz file?
>
> Thanks,
> Noam
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>
>
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[Freesurfer] path.pd.trk format

[Peled, Noam]

Hello,
I've noticed that in tracula 5.2 there's also a path.pd.trk file in the output 
directory.
How can I read this file? I would like to read the actual splines and not the 
probabilistic distribution in path.pd.nii.gz.

Thanks,
Noam Peled
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Re: [Freesurfer] path.pd.trk format

[Peled, Noam]

I've found an 
example<https://mail.python.org/pipermail/neuroimaging/2015-September/000488.html>
 how to read trk file with nibabel:

> import nibabel as nib
>
> track_gen, hdr = nib.trackvis.read(trk_file, as_generator=True)
>
> tracks = []
> while True:
> try:
> track = next(track_gen)
> except (StopIteration, TypeError):
> break
> tracks.append(track)


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Peled, Noam 
[npe...@mgh.harvard.edu]
Sent: Tuesday, February 16, 2016 2:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] path.pd.trk format

Hello,
I've noticed that in tracula 5.2 there's also a path.pd.trk file in the output 
directory.
How can I read this file? I would like to read the actual splines and not the 
probabilistic distribution in path.pd.nii.gz.

Thanks,
Noam Peled
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Re: [Freesurfer] path.pd.trk format

[Peled, Noam]

Thanks!
Do you in which space are the voxel coordinates coordinates? Are they in the 
diffusion space? 

Thanks again,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Saturday, March 05, 2016 5:10 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] path.pd.trk format

Hi Noam - You can read the .trk file with trackvis. It contains all the
path samples that are added up to created the probability distribution of
the path. Please keep in mind, however, that this .trk file is just meant
for generating stats and not for visualization, so these are not the usual
smoothed kind of streamlines that you get from deterministic tractography.
It contains only integer voxel coordinates, so the streamlines will look
sort of like step ladders if you visualize them.

Best,

a.y

On Tue, 16 Feb 2016, Peled, Noam wrote:

> Hello,
> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
> output directory.
> How can I read this file? I would like to read the actual splines and not the 
> probabilistic distribution in path.pd.nii.gz.
>
> Thanks,
> Noam Peled
>
>
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Re: [Freesurfer] path.pd.trk format

[Peled, Noam]

So for plotting the fibers, like in freeview, should I just use the 
/dmri/xfms/diff2anatorig..mat or 
/dmri/xfms/diff2anat..mat transformation matrices?

Thanks again,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Monday, March 07, 2016 12:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] path.pd.trk format

Yes, native diffusion space.

On Mon, 7 Mar 2016, Peled, Noam wrote:

> Thanks!
> Do you in which space are the voxel coordinates coordinates? Are they in the 
> diffusion space?
>
> Thanks again,
> Noam
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Saturday, March 05, 2016 5:10 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> Hi Noam - You can read the .trk file with trackvis. It contains all the
> path samples that are added up to created the probability distribution of
> the path. Please keep in mind, however, that this .trk file is just meant
> for generating stats and not for visualization, so these are not the usual
> smoothed kind of streamlines that you get from deterministic tractography.
> It contains only integer voxel coordinates, so the streamlines will look
> sort of like step ladders if you visualize them.
>
> Best,
>
> a.y
>
> On Tue, 16 Feb 2016, Peled, Noam wrote:
>
>> Hello,
>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
>> output directory.
>> How can I read this file? I would like to read the actual splines and not 
>> the probabilistic distribution in path.pd.nii.gz.
>>
>> Thanks,
>> Noam Peled
>>
>>
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Re: [Freesurfer] path.pd.trk format

[Peled, Noam]

I want to display it in my new 3d visualization tool, along the hemispheres and 
the subcortical regions.
The hemispheres and the subcortical regions I import from freesurfer.

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Monday, March 07, 2016 12:20 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] path.pd.trk format

What to you want to display it on? If you want to display in on the FA
map, or anything that's in diffusion space, you don't need any transform.

On Mon, 7 Mar 2016, Peled, Noam wrote:

> So for plotting the fibers, like in freeview, should I just use the 
> /dmri/xfms/diff2anatorig..mat or 
> /dmri/xfms/diff2anat..mat transformation matrices?
>
> Thanks again,
> Noam
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Monday, March 07, 2016 12:09 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] path.pd.trk format
>
> Yes, native diffusion space.
>
> On Mon, 7 Mar 2016, Peled, Noam wrote:
>
>> Thanks!
>> Do you in which space are the voxel coordinates coordinates? Are they in the 
>> diffusion space?
>>
>> Thanks again,
>> Noam
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
>> [ayend...@nmr.mgh.harvard.edu]
>> Sent: Saturday, March 05, 2016 5:10 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] path.pd.trk format
>>
>> Hi Noam - You can read the .trk file with trackvis. It contains all the
>> path samples that are added up to created the probability distribution of
>> the path. Please keep in mind, however, that this .trk file is just meant
>> for generating stats and not for visualization, so these are not the usual
>> smoothed kind of streamlines that you get from deterministic tractography.
>> It contains only integer voxel coordinates, so the streamlines will look
>> sort of like step ladders if you visualize them.
>>
>> Best,
>>
>> a.y
>>
>> On Tue, 16 Feb 2016, Peled, Noam wrote:
>>
>>> Hello,
>>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the 
>>> output directory.
>>> How can I read this file? I would like to read the actual splines and not 
>>> the probabilistic distribution in path.pd.nii.gz.
>>>
>>> Thanks,
>>> Noam Peled
>>>
>>>
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>>
>>
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[Freesurfer] preproc-sess - Cannot allocate memory

[Peled, Noam]

Hey all,
I'm running preproc-sess, and getting the following error:
...
Reading in mov rest/tmp.bbregister.28405/template.nii
Reading in ref .../mri/brainmask.mgz
Reading in and applying refmask .../mri/aparc+aseg.mgz
Cannot allocate memory

I checked, and the aparc+aseg.mgz file is ok (I can read it with nibabel)

I'm using the FreeSurfer dev version 
(freesurfer-Linux-centos6_x86_64-dev-20161215-dd925e2) on a
32GB CentOs7 machine, so I don't think I'm really out of memory.

Thanks,
Noam
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[Freesurfer] Yet another freeview coordinates question

[Peled, Noam]

Hey all,
When loading two T1 in freeview, one for a subject and one for fsaverage, and 
switching between them, only the tkreg RAS coordinates changes while moving the 
mouse, not the RAS.
Does it mean that the RAS in freeview is always in MNI305?

Thanks,
Noam
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Re: [Freesurfer] Yet another freeview coordinates question

[Peled, Noam]

ok, I've figured out that this is indeed the case:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23348.html

Also, following these instructions I was able to get RAS from the tkreg RAS in 
FreeView:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024293.html

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Peled, Noam 
[npe...@mgh.harvard.edu]
Sent: Wednesday, March 08, 2017 9:27 AM
To: Freesurfer support list ‎[freesurfer@nmr.mgh.harvard.edu]‎
Subject: [Freesurfer] Yet another freeview coordinates question

Hey all,
When loading two T1 in freeview, one for a subject and one for fsaverage, and 
switching between them, only the tkreg RAS coordinates changes while moving the 
mouse, not the RAS.
Does it mean that the RAS in freeview is always in MNI305?

Thanks,
Noam
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[Freesurfer] morphing ?h.cortex.patch.flat to sample subject

[Peled, Noam]

Hey all
I'm trying to morph the fsaverage flat patch (?h.cortex.patch.flat) to the 
freesurfer sample subject, and getting the following error:

mri_surf2surf --srcsubject fsaverage --srcsurfval lh.cortex.patch.flat 
--trgsubject sample --trgsurfval lh.cortex.patch.sample.flat --hemi lh
ERROR: could not determine type of lh.cortex.patch.sample.flat

mris_convert also didn't work:
mri_surf2surf --srcsubject fsaverage --srcsurfval lh.cortex.patch.flat 
--trgsubject sample --trgsurfval lh.cortex.patch.sample.flat --hemi lh
ERROR: could not determine type of lh.cortex.patch.sample.flat
[thibault:surf] (nmr-stable53-env) mris_convert lh.cortex.patch.flat 
lh.cortex.patch.flat.asc
mrisFindNeighbors: lh.cortex.patch.flat: face[0].v[0] = 0, but face 0 not in 
vertex 0 face list

I could read it using the python code in pyCortex:
https://github.com/gallantlab/pycortex/blob/00cc7dadd16149ac7f6fe38621c95c43c4b71cad/cortex/freesurfer.py#L189

And after that save it as a freesurfer surface:
https://github.com/gallantlab/pycortex/blob/00cc7dadd16149ac7f6fe38621c95c43c4b71cad/cortex/freesurfer.py#L167

But even after that mri_surf2surf couldn't determine the type.

Any ideas?
Thanks,
Noam



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[Freesurfer] Transforming invasive electrodes coordinates to a template brain

[Peled, Noam]

Dear freesurfer experts,

I would like to present invasive electrodes from different subjects in the same 
template brain.

I thought about doing a volumetric registration (all the electrodes are depth) 
using mri_cvs_register:

mri_cvs_register --mov {subject} --template {template} --outdir 
$SUBJECTS_DIR/{template}/mri_cvs_register --step3

And then using mri_vol2vol that'll use the resulting m3z transformation file.

Can I do it for a list of coordinates?


Thanks,

Noam
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Re: [Freesurfer] Nonlinear CVS registration into average brain for coordinates

[Peled, Noam]

Hey David,

Have you managed to find a solution for that?


Best,

Noam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zhou, David Wei 

Sent: Thursday, April 7, 2016 3:10:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Nonlinear CVS registration into average brain for 
coordinates

Hi all,

I have a data set of 14 subjects with intracranial (both cortical and 
subcortical) electrode implants, already recon'ed in Freesurfer, with an 
average brain + surface computed of these subjects. I would like to map each 
subject's electrode coordinates (a set of RAS points) into the average brain 
using a nonlinear transformation to account for individual deviations in 
surface topology.

I'm trying to figure out the steps that must be taken to achieve this. With my 
average brain as a template, it seems like I would use mri_cvs_register to 
produce each subject warped onto the template. After generating those warps, 
how does one apply the same warp to a set of coordinates, for example to find 
out where my electrodes end up in the template brain? Which output file in 
.../cvs contains the data necessary to compute the coordinates in the template?

I'd appreciate any instruction, thanks!

David
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Re: [Freesurfer] Skull as an Object

[Peled, Noam]

Sure!

You can find all about it in mmvt.org

We also have a special panel for the skull:

https://github.com/pelednoam/mmvt/wiki/Skull-panel


Best,

Noam


From: Matti Hamalainen 
Sent: Saturday, July 21, 2018 1:53:15 PM
To: Bruce Fischl
Cc: Freesurfer support list; Peled, Noam
Subject: Re: [Freesurfer] Skull as an Object

Hi Alex,

Noam Peled (npe...@mgh.harvard.edu<mailto:npe...@mgh.harvard.edu>) can help you 
with this because he is using Blender in his MMVT. - Matti

On Jul 21, 2018, at 1:45 PM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:

Hi Alex

I'm not entirely sure what you mean. We do output boundary element models of 
the skull interfaces for MEG/EEG analysis if that is of interest. Matti 
Hamalainen can point you in the right direction for obtaining those models if 
you want

cheers
Bruce

On Mon, 16 Jul 2018, Zhang, Alexander D wrote:

Good Morning Freesurfer experts,
I am trying to get the brain and skull as separate objects for use in blender. 
Is there any way to
retain the skull in freesurfer?
If not, would it be possible to retain all the mapping from the skullstrip 
feature?
Best,
- Alex




-

Matti Hamalainen, Ph.D.
Professor of Radiology, Harvard Medical School

Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Building 149, 13th Street, Mailcode 149-2301
Charlestown, MA 02129-2060
USA

e-mail  m...@nmr.mgh.harvard.edu<mailto:m...@nmr.mgh.harvard.edu>
Tel +1 617 726 0323
FAX +1 617 726 7422






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[Freesurfer] mri_cvs_register using fsaverage

[Peled, Noam]

I need to transfer one of our patient's electrodes locations (depth electrodes, 
they aren't located on the cortical surface) to MNI305 space.
For that, I'm trying to use mri_cvs_register to register the patient to 
fsaverage. I'm using to the following command:


mri_cvs_register --mov subjid --template fsaverage --outdir output_name 
--nocleanup

And I'm getting the following error:
fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, .K)

Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
Any ideas?

Thanks,
Noam







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Re: [Freesurfer] mri_cvs_register using fsaverage

[Peled, Noam]

Thanks Lilla!

Just to be sure, when using the --mni flag, should I remove the  --template 
flag?

Also, is there any way I can calculate the registration directly to MNI305 and 
not MNI152?


Thanks again,

Noam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lilla Zollei 

Sent: Wednesday, August 1, 2018 8:35:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage


Hi Noam,

Can you can use the --mni flag?

"Use the CVS atlas in MNI152 space as a target for registration (as
opposed to the default CVS template)"

Lilla

On Wed, 1 Aug 2018, Peled, Noam wrote:

>
> I need to transfer one of our patient's electrodes locations (depth 
> electrodes, they aren't located on the cortical surface) to MNI305 space.
> For that, I'm trying to use mri_cvs_register to register the patient to 
> fsaverage. I'm using to the following command:
>
>
> mri_cvs_register --mov subjid --template fsaverage --outdir output_name 
> --nocleanup
>
> And I'm getting the following error:
> fsaverage : at least one mean and/or Gaussian curvature file is missing (.H, 
> .K)
>
> Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
> Any ideas?
>
> Thanks,
> Noam
>
>
>
>
>
>
>
>
>
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] mri_cvs_register using fsaverage

[Peled, Noam]

Thanks for the clarification, I'm asking that because in the mri_cvs_register 
docs it's written that the --mni flag will "use the CVS atlas in MNI152 space 
as a target for registration".


Thanks again,

Noam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Wednesday, August 1, 2018 11:19:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage

FYI, fsaverage is already in MNI305 space

On 08/01/2018 11:14 AM, Peled, Noam wrote:
>
> Thanks Lilla!
>
> Just to be sure, when using the --mni flag, should I remove the
> --template flag?
>
> Also, is there any way I can calculate the registration directly to
> MNI305 and not MNI152?
>
>
> Thanks again,
>
> Noam
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Lilla Zollei
> 
> *Sent:* Wednesday, August 1, 2018 8:35:49 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] mri_cvs_register using fsaverage
>
> Hi Noam,
>
> Can you can use the --mni flag?
>
> "Use the CVS atlas in MNI152 space as a target for registration (as
> opposed to the default CVS template)"
>
> Lilla
>
> On Wed, 1 Aug 2018, Peled, Noam wrote:
>
> >
> > I need to transfer one of our patient's electrodes locations (depth
> electrodes, they aren't located on the cortical surface) to MNI305 space.
> > For that, I'm trying to use mri_cvs_register to register the patient
> to fsaverage. I'm using to the following command:
> >
> >
> > mri_cvs_register --mov subjid --template fsaverage --outdir
> output_name --nocleanup
> >
> > And I'm getting the following error:
> > fsaverage : at least one mean and/or Gaussian curvature file is
> missing (.H, .K)
> >
> > Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
> > Any ideas?
> >
> > Thanks,
> > Noam
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] mri_cvs_register using fsaverage

[Peled, Noam]

Thanks Lilla!

A follow-up question: How can I use the applyMorph function to morph the points 
to the MNI152 space?

I'm trying to use the combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d 
file I've got from the mri_cvs_register call.

Which template should I use? I can't use fsaverage because it's in the MNI305 
space. Should I use cvs_avg35_inMNI152 instead?

And to morph it to MNI305, should I use the inverse matrix of

M = [[0.9975, - 0.0073, 0.0176, -0.0429],
 [0.0146, 1.0009, -0.0024, 1.5496],
 [-0.0130, -0.0093, 0.9971, 1.1840],
 [0, 0, 0, 1.]]

As mentioned in the last section in 
http://freesurfer.net/fswiki/CoordinateSystems?


Thanks!

Noam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lilla Zollei 

Sent: Wednesday, August 1, 2018 2:33:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage


Yes, you can remove the template flag.

And no, not at the moment.

> Thanks Lilla!
>
> Just to be sure, when using the --mni flag, should I remove the  --template 
> flag?
>
> Also, is there any way I can calculate the registration directly to MNI305 
> and not MNI152?
>
>
> Thanks again,
>
> Noam
>
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Lilla Zollei 
> 
> Sent: Wednesday, August 1, 2018 8:35:49 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_cvs_register using fsaverage
>
> Hi Noam,
>
> Can you can use the --mni flag?
>
> "Use the CVS atlas in MNI152 space as a target for registration (as
> opposed to the default CVS template)"
>
> Lilla
>
> On Wed, 1 Aug 2018, Peled, Noam wrote:
>
> >
> > I need to transfer one of our patient's electrodes locations (depth 
> > electrodes, they aren't located on the cortical surface) to MNI305 space.
> > For that, I'm trying to use mri_cvs_register to register the patient to 
> > fsaverage. I'm using to the following command:
> >
> >
> > mri_cvs_register --mov subjid --template fsaverage --outdir output_name 
> > --nocleanup
> >
> > And I'm getting the following error:
> > fsaverage : at least one mean and/or Gaussian curvature file is missing 
> > (.H, .K)
> >
> > Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
> > Any ideas?
> >
> > Thanks,
> > Noam
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
>
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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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Re: [Freesurfer] mri_cvs_register using fsaverage

[Peled, Noam]

It doesn't seem to work

Here  are the commands I was using:

mri_cvs_register --mov $SUBJECT --mni --outdir 
$SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni --nocleanup
applyMorph --template $SUBJECTS_DIR/cvs_avg35_inMNI152/mri/orig.mgz
   --transform 
$SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d
   point_list $SUBJECTS_DIR/$SUBJECT/electrodes/electrodes_to_morph.txt 
$SUBJECTS_DIR/$SUBJECT/electrodes/electrodes_morph_to_MNI152.txt a

The file electrodes_to_morph.txt contains the electrodes in the $SUBJECT's orig 
space (T1 voxels)
As a sanity check, I checked the electrodes' values in brainmask.mgz. When 
checking the electrodes in electrodes_to_morph.txt against 
$SUBJECT/mri/brainmask.mgz, only a few were outside the brain. But when 
checking the electrodes after the morphing in electrodes_morph_to_MNI152.txt 
against  cvs_avg35_inMNI152/mri/brainmask.mgz, at least half of them were 
outside the brain.

Any ideas?
Thanks,
Noam


____
From: Peled, Noam
Sent: Saturday, August 18, 2018 3:08:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage


Thanks Lilla!

A follow-up question: How can I use the applyMorph function to morph the points 
to the MNI152 space?

I'm trying to use the combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d 
file I've got from the mri_cvs_register call.

Which template should I use? I can't use fsaverage because it's in the MNI305 
space. Should I use cvs_avg35_inMNI152 instead?

And to morph it to MNI305, should I use the inverse matrix of

M = [[0.9975, - 0.0073, 0.0176, -0.0429],
 [0.0146, 1.0009, -0.0024, 1.5496],
 [-0.0130, -0.0093, 0.9971, 1.1840],
 [0, 0, 0, 1.]]

As mentioned in the last section in 
http://freesurfer.net/fswiki/CoordinateSystems?


Thanks!

Noam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lilla Zollei 

Sent: Wednesday, August 1, 2018 2:33:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage


Yes, you can remove the template flag.

And no, not at the moment.

> Thanks Lilla!
>
> Just to be sure, when using the --mni flag, should I remove the  --template 
> flag?
>
> Also, is there any way I can calculate the registration directly to MNI305 
> and not MNI152?
>
>
> Thanks again,
>
> Noam
>
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Lilla Zollei 
> 
> Sent: Wednesday, August 1, 2018 8:35:49 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_cvs_register using fsaverage
>
> Hi Noam,
>
> Can you can use the --mni flag?
>
> "Use the CVS atlas in MNI152 space as a target for registration (as
> opposed to the default CVS template)"
>
> Lilla
>
> On Wed, 1 Aug 2018, Peled, Noam wrote:
>
> >
> > I need to transfer one of our patient's electrodes locations (depth 
> > electrodes, they aren't located on the cortical surface) to MNI305 space.
> > For that, I'm trying to use mri_cvs_register to register the patient to 
> > fsaverage. I'm using to the following command:
> >
> >
> > mri_cvs_register --mov subjid --template fsaverage --outdir output_name 
> > --nocleanup
> >
> > And I'm getting the following error:
> > fsaverage : at least one mean and/or Gaussian curvature file is missing 
> > (.H, .K)
> >
> > Indeed, fsaverage doesn't have the rh/lh.inflated.K/H files.
> > Any ideas?
> >
> > Thanks,
> > Noam
> >
> >
> >
> >
> >
> >
> >
> >
> >
>
>
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_cvs_register using fsaverage

[Peled, Noam]

Thanks Lilla!

I'm working with the dev version on my laptop, but indeed I've downloaded it 
before the patch. I've updated the version and now everything is working!


Thanks so much,

Noam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lilla Zollei 

Sent: Sunday, August 19, 2018 3:16:31 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage


Hi Noam,

What version of FS are you using? I have incorporated a change into dev in
January. Have you seen this note?

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-January/055460.html

Lilla

On Sat, 18 Aug 2018, Peled, Noam wrote:

>
> It doesn't seem to work
>
> Here  are the commands I was using:
>
>
> mri_cvs_register --mov $SUBJECT --mni --outdir 
> $SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni --nocleanup
> applyMorph --template $SUBJECTS_DIR/cvs_avg35_inMNI152/mri/orig.mgz
>--transform 
> $SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d
>point_list $SUBJECTS_DIR/$SUBJECT/electrodes/electrodes_to_morph.txt 
> $SUBJECTS_DIR/$SUBJECT/electrodes/electrodes_morph_to_MNI152.txt a
>
> The file electrodes_to_morph.txt contains the electrodes in the $SUBJECT's 
> orig space (T1 voxels)
> As a sanity check, I checked the electrodes' values in brainmask.mgz. When 
> checking the electrodes in electrodes_to_morph.txt against 
> $SUBJECT/mri/brainmask.mgz, only a few were outside the brain.
> But when checking the electrodes after the morphing in 
> electrodes_morph_to_MNI152.txt against  cvs_avg35_inMNI152/mri/brainmask.mgz, 
> at least half of them were outside the brain.
>
> Any ideas?
> Thanks,
> Noam
>
> ______
> From: Peled, Noam
> Sent: Saturday, August 18, 2018 3:08:22 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_cvs_register using fsaverage
>
> Thanks Lilla!
>
> A follow-up question: How can I use the applyMorph function to morph the 
> points to the MNI152 space?
>
> I'm trying to use the combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d 
> file I've got from the mri_cvs_register call.
>
> Which template should I use? I can't use fsaverage because it's in the MNI305 
> space. Should I use cvs_avg35_inMNI152 instead?
>
> And to morph it to MNI305, should I use the inverse matrix of
>
> M = [[0.9975, - 0.0073, 0.0176, -0.0429],
>  [0.0146, 1.0009, -0.0024, 1.5496],
>  [-0.0130, -0.0093, 0.9971, 1.1840],
>  [0, 0, 0, 1.]]
> As mentioned in the last section in 
> http://freesurfer.net/fswiki/CoordinateSystems?
>
>
> Thanks!
>
> Noam
>
>
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Lilla Zollei 
> 
> Sent: Wednesday, August 1, 2018 2:33:19 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_cvs_register using fsaverage
>
> Yes, you can remove the template flag.
>
> And no, not at the moment.
>
> > Thanks Lilla!
> >
> > Just to be sure, when using the --mni flag, should I remove the  --template 
> > flag?
> >
> > Also, is there any way I can calculate the registration directly to MNI305 
> > and not MNI152?
> >
> >
> > Thanks again,
> >
> > Noam
> >
> >_
> _
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> >  on behalf of Lilla Zollei 
> > 
> > Sent: Wednesday, August 1, 2018 8:35:49 AM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] mri_cvs_register using fsaverage
> >
> > Hi Noam,
> >
> > Can you can use the --mni flag?
> >
> > "Use the CVS atlas in MNI152 space as a target for registration (as
> > opposed to the default CVS template)"
> >
> > Lilla
> >
> > On Wed, 1 Aug 2018, Peled, Noam wrote:
> >
> > >
> > > I need to transfer one of our patient's electrodes locations (depth 
> > > electrodes, they aren't located on the cortical surface) to MNI305 space.

[Freesurfer] applyMorph gives (10000 10000 10000) coordinates

[Peled, Noam]

Hey all,
I'm trying to morph patients' invasive electrodes into a template brain.
I'm not sure why, but sometimes, the applyMorph gives me the (1 1 
1) coordinates for a subset of the electrodes, where the rest are ok.
In the output, for those electrodes I can see it writes "not valid", but still 
gives reasonable coordinates and not (1 1 1)
For example:

applyMorph --template 
/autofs/space/thibault_001/users/npeled/subjects/colin27/mri/orig.mgz 
--transform 
/autofs/space/thibault_001/users/npeled/subjects/MG106/mri_cvs_register_to_colin27/combined_tocolin27_elreg_afteraseg-norm.tm3d
 point_list 
/autofs/space/thibault_001/users/npeled/subjects/MG106/electrodes/electrodes_to_morph.txt
 
/autofs/space/thibault_001/users/npeled/mmvt/MG106/electrodes/electrodes_morph_to_colin27.txt
 a

Where in the output file you can see the (1 1 1)  coordinates.
I attached the applyMorph output.
btw, I'm using the Freesurfer dev version

Thanks,
Noam


LZ


Template 
name:/local_mount/space/thibault/1/users/npeled/subjects/colin27/mri/orig.mgz
After loading template
Template 
name:/local_mount/space/thibault/1/users/npeled/subjects/colin27/mri/orig.mgz
After loading template
 extension = tm3d
 data size = 144945311
 uilen = 6
 loading transform id string = 
 data size = 148594983
 uilen = 6
 loading transform id string = 
 data size = 16
 uilen = 3
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 25
 uilen = 6
 loading transform id string = 
 data size = 71
 uilen = 7
 loading transform id string = 
 loaded transform
 executing filter on file 
/local_mount/space/thibault/1/users/npeled/subjects/MG106/electrodes/electrodes_to_morph.txt
 The number of lines in the input file is 214
 computing image for point 127 115 177
 = 130.881 159.835 48.9774
valid
 computing image for point 130 115 177
 = 133.607 160.851 48.71
valid
 computing image for point 133 115 177
 = 135.946 162.356 47.661
valid
 computing image for point 137 115 177
 = 139.09 162.775 46.8734
valid
 computing image for point 141 115 177
 = 140.297 163.009 46.2098
valid
 computing image for point 144 115 177
 = 142.3 161.281 44.3398
valid
 computing image for point 148 115 177
 = 145.84 161.603 42.0473
valid
 computing image for point 151 115 177
 = 147.368 159.362 42.2778
valid
 computing image for point 155 115 177
 = 152.428 159.408 41.8632
valid
 computing image for point 158 114 177
 = 154.842 157.229 40.359
valid
 computing image for point 162 114 177
 = 159.988 156.492 41.0982
valid
 computing image for point 166 113 177
 = 167.409 154.575 42.0068
valid
 computing image for point 169 114 179
 = 174.403 155.768 43.8384
valid
 computing image for point 171 114 179
 = 177.166 155.691 44.0198
valid
 computing image for point 124 121 185
 = 129.922 164.841 51.8364
valid
 computing image for point 127 119 185
 = 134.632 164 53.0312
valid
 computing image for point 130 118 185
 = 136.759 164.935 54.4396
valid
 computing image for point 134 117 184
 = 138.824 165.956 51.7842
valid
 computing image for point 138 115 184
 = 140.943 164.89 50.5941
valid
 computing image for point 141 115 184
 = 142.655 162.795 50.3766
valid
 computing image for point 145 114 183
 = 146.188 161.687 50.2295
valid
 computing image for point 148 112 183
 = 152.797 160.582 50.1051
valid
 computing image for point 151 113 183
 = 153.284 159.745 48.5842
valid
 computing image for point 155 111 182
 = 159.225 156.275 46.775
valid
 computing image for point 158 110 182
 = 165.496 154.288 46.7171
valid
 computing image for point 162 109 182
 = 171.434 150.812 46.8667
valid
 computing image for point 129 105 148
 = 130.602 123.757 2.28372
valid
 computing image for point 131 104 148
 = 13

Re: [Freesurfer] applyMorph gives (10000 10000 10000) coordinates

[Peled, Noam]

Hey Lila,
Sorry for the confusion, the attached file is the terminal output.
Please find also the applyMorph output file.

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lilla Zollei 

Sent: Thursday, February 7, 2019 10:31 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] applyMorph gives (1 1 1) coordinates


Hi Noam,

Maybe a I am a bit confused but in the attached file I do not see the
(1 1 1) coordinate that correspond to invalid coordinate
locations. Is the file that you attached your
electrodes_morph_to_colin27.txt or is it the terminal output?

Lilla

On Thu, 7 Feb 2019, Peled, Noam wrote:

> Hey all,
> I'm trying to morph patients' invasive electrodes into a template brain.
> I'm not sure why, but sometimes, the applyMorph gives me the (1 1 
> 1) coordinates for a subset of the electrodes, where the rest are ok.
> In the output, for those electrodes I can see it writes "not valid", but 
> still gives reasonable coordinates and not (1 1 1)
> For example:
>
> applyMorph --template 
> /autofs/space/thibault_001/users/npeled/subjects/colin27/mri/orig.mgz 
> --transform 
> /autofs/space/thibault_001/users/npeled/subjects/MG106/mri_cvs_register_to_colin27/combined_tocolin27_elreg_afteraseg-norm.tm3d
>  point_list
> /autofs/space/thibault_001/users/npeled/subjects/MG106/electrodes/electrodes_to_morph.txt
>  
> /autofs/space/thibault_001/users/npeled/mmvt/MG106/electrodes/electrodes_morph_to_colin27.txt
>  a
>
> Where in the output file you can see the (1 1 1)  coordinates.
> I attached the applyMorph output.
> btw, I'm using the Freesurfer dev version
>
> Thanks,
> Noam
>
> 
> LZ
>
>
>
>
130.881 159.835 48.9774
133.607 160.851 48.71
135.946 162.356 47.661
139.09 162.775 46.8734
140.297 163.009 46.2098
142.3 161.281 44.3398
145.84 161.603 42.0473
147.368 159.362 42.2778
152.428 159.408 41.8632
154.842 157.229 40.359
159.988 156.492 41.0982
167.409 154.575 42.0068
174.403 155.768 43.8384
177.166 155.691 44.0198
129.922 164.841 51.8364
134.632 164 53.0312
136.759 164.935 54.4396
138.824 165.956 51.7842
140.943 164.89 50.5941
142.655 162.795 50.3766
146.188 161.687 50.2295
152.797 160.582 50.1051
153.284 159.745 48.5842
159.225 156.275 46.775
165.496 154.288 46.7171
171.434 150.812 46.8667
130.602 123.757 2.28372
132.657 122.529 2.8569
137.256 122.647 3.15639
139.569 121.95 5.38376
142.451 122.084 5.83202
145.114 120.873 7.05031
147.037 120.978 7.60215
149.259 120.297 10.7982
151.233 121.722 10.8858
153.359 120.351 13.0719
155.425 119.57 17.1487
157.149 121.151 17.8223
159.13 121.461 18.9834
162.404 120.604 21.2537
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
143.309 145.999 -3.64764
145.121 141.529 -3.65274
145.895 138.953 -3.5807
146.847 134.406 -3.56003
147.56 131.788 -3.36578
148.4 127.276 -3.13
148.981 124.631 -2.39035
150.407 120.145 -1.75338
150.998 115.568 -1.0397
151.68 112.325 -0.674474
152.45 107.967 1.72525
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
109.162 160.775 34.1574
105.629 161.13 32.8198
104.065 160.794 29.8431
101.245 160.722 29.0729
99.3541 160.71 28.8086
97.5758 159.691 26.886
96.1602 157.311 25.2255
94.5445 157.029 25.3677
93.3807 155.97 23.9477
91.4864 154.723 22.73
89.2752 154.299 23.3965
86.6756 154.565 25.685
106.485 165.677 53.5792
102.221 165.966 53.7515
100.39 166.443 55.1393
99.0081 166.718 54.6491
95.5373 165.239 52.3683
93.4939 163.296 51.1699
90.5296 161.12 49.5121
92.3594 157.249 47.6697
92.7311 158.944 47.9095
91.5857 158.36 47.0339
93.7978 151.437 45.2223
91.3165 150.531 45.4054
112.982 123.396 5.90744
111.053 123.249 5.70934
106.828 122.256 3.86287
104.797 118.843 3.47794
102.663 118.57 3.46022
99.7506 117.777 2.341
96.7199 117.025 1.54502
94.651 116.774 2.01279
92.5808 114.641 2.19245
90.4561 112.738 4.09428
88.3815 112 4.2304
85.7062 111.174 5.09489
83.4357 110.436 5.60522
82.1138 110.28 6.53095
1 1 1
1 1 1
10

Re: [Freesurfer] applyMorph gives (10000 10000 10000) coordinates

[Peled, Noam]

Another strange thing, one of the points (voxels) I'm trying to morph is 149 
137 108. In Freeview, this coordinate is in the left hippocampus. When applying 
the morphing to our template brain, this is the terminal output:
computing image for point 149 137 108
 = 141.143 151.458 11.3095
But (141 151 11)  is outside the template's brain.

For the registration, I'm using the following command:
mri_cvs_register --mov MG122 --template colin27 --outdir 
/home/cashlab/mmvt_root/subjects/MG122/mri_cvs_register_to_colin27 --nocleanup 
--openmp 8

For applying it on the electrodes:
mri_cvs_register --mov MG122 --template colin27 --outdir 
/local_mount/space/thibault/1/users/npeled/subjects/MG122/mri_cvs_register_to_colin27
 --nocleanup --openmp 8

And for applying it on the electrodes file:
applyMorph --template 
/autofs/space/thibault_001/users/npeled/subjects/colin27/mri/orig.mgz 
--transform 
/autofs/space/thibault_001/users/npeled/subjects/MG122/mri_cvs_register_to_colin27/combined_tocolin27_elreg_afteraseg-norm.tm3d
 point_list 
/autofs/space/thibault_001/users/npeled/subjects/MG122/electrodes/electrodes_to_morph.txt
 
/autofs/space/thibault_001/users/npeled/mmvt/MG122/electrodes/electrodes_morph_to_colin27.txt
 a

Am I missing something?
Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Peled, Noam 

Sent: Thursday, February 7, 2019 10:36 AM
To: Lilla Zollei; Freesurfer support list
Subject: Re: [Freesurfer] applyMorph gives (1 1 1) coordinates

Hey Lila,
Sorry for the confusion, the attached file is the terminal output.
Please find also the applyMorph output file.

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lilla Zollei 

Sent: Thursday, February 7, 2019 10:31 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] applyMorph gives (1 1 1) coordinates


Hi Noam,

Maybe a I am a bit confused but in the attached file I do not see the
(1 1 1) coordinate that correspond to invalid coordinate
locations. Is the file that you attached your
electrodes_morph_to_colin27.txt or is it the terminal output?

Lilla

On Thu, 7 Feb 2019, Peled, Noam wrote:

> Hey all,
> I'm trying to morph patients' invasive electrodes into a template brain.
> I'm not sure why, but sometimes, the applyMorph gives me the (1 1 
> 1) coordinates for a subset of the electrodes, where the rest are ok.
> In the output, for those electrodes I can see it writes "not valid", but 
> still gives reasonable coordinates and not (1 1 1)
> For example:
>
> applyMorph --template 
> /autofs/space/thibault_001/users/npeled/subjects/colin27/mri/orig.mgz 
> --transform 
> /autofs/space/thibault_001/users/npeled/subjects/MG106/mri_cvs_register_to_colin27/combined_tocolin27_elreg_afteraseg-norm.tm3d
>  point_list
> /autofs/space/thibault_001/users/npeled/subjects/MG106/electrodes/electrodes_to_morph.txt
>  
> /autofs/space/thibault_001/users/npeled/mmvt/MG106/electrodes/electrodes_morph_to_colin27.txt
>  a
>
> Where in the output file you can see the (1 1 1)  coordinates.
> I attached the applyMorph output.
> btw, I'm using the Freesurfer dev version
>
> Thanks,
> Noam
>
> 
> LZ
>
>
>
>
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Re: [Freesurfer] applyMorph gives (10000 10000 10000) coordinates

[Peled, Noam]

Sure!
Do you want the T1, or also the mri_cvs_register outputs?
btw, I'm in the martinos, so you can access all my files (I wrote the full path)

Many thanks,
Noam

p.s I'm using two different computers, one of them isn't in the center, and the 
freesurfer's version is
freesurfer-linux-centos6_x86_64-dev-20180622-7758bad
(hmmm, should I be worried it ends with 'bad'?)
Can it cause these kinds of problems?



From: Lilla Zollei 
Sent: Thursday, February 7, 2019 2:04 PM
To: Peled, Noam
Cc: Freesurfer support list
Subject: Re: [Freesurfer] applyMorph gives (1 1 1) coordinates


Hi Noam, Would it be possible fo ryou to upload a sample data set to our
filesharing site?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Lilla

On Thu, 7 Feb 2019, Peled, Noam wrote:

> Hey Lila,
> Sorry for the confusion, the attached file is the terminal output.
> Please find also the applyMorph output file.
>
> Thanks,
> Noam
>
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Lilla Zollei 
> 
> Sent: Thursday, February 7, 2019 10:31 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] applyMorph gives (1 1 1) coordinates
>
> Hi Noam,
>
> Maybe a I am a bit confused but in the attached file I do not see the
> (1 1 1) coordinate that correspond to invalid coordinate
> locations. Is the file that you attached your
> electrodes_morph_to_colin27.txt or is it the terminal output?
>
> Lilla
>
> On Thu, 7 Feb 2019, Peled, Noam wrote:
>
> > Hey all,
> > I'm trying to morph patients' invasive electrodes into a template brain.
> > I'm not sure why, but sometimes, the applyMorph gives me the (1 1 
> > 1) coordinates for a subset of the electrodes, where the rest are ok.
> > In the output, for those electrodes I can see it writes "not valid", but 
> > still gives reasonable coordinates and not (1 1 1)
> > For example:
> >
> > applyMorph --template 
> > /autofs/space/thibault_001/users/npeled/subjects/colin27/mri/orig.mgz 
> > --transform 
> > /autofs/space/thibault_001/users/npeled/subjects/MG106/mri_cvs_register_to_colin27/combined_tocolin27_elreg_afteraseg-norm.tm3d
> >  point_list
> > /autofs/space/thibault_001/users/npeled/subjects/MG106/electrodes/electrodes_to_morph.txt
> >  
> > /autofs/space/thibault_001/users/npeled/mmvt/MG106/electrodes/electrodes_morph_to_colin27.txt
> >  a
> >
> > Where in the output file you can see the (1 1 1)  coordinates.
> > I attached the applyMorph output.
> > btw, I'm using the Freesurfer dev version
> >
> > Thanks,
> > Noam
> >
> > 
> > LZ
> >
> >
> >
> >
>
>
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[Freesurfer] recon-all: making sure that brain.mgz will be in RAS orientation.

[Peled, Noam]

Dear group,
I ran recon-all on a T1 nii file, which is in LAS orientation. The brain.mgz 
turn out to be in LIA orientation.
I've tried to convert the nii file to RAS (mri_convert --in_orientation LAS 
--out_orientation RAS ...), and rerun recon-all, but it didn't change the 
results.
How do I make sure my output files will be in RAS orientation?

Thanks,
Noam
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Re: [Freesurfer] recon-all: making sure that brain.mgz will be in RAS orientation.

[Peled, Noam]

Hey Bruce.
Originally this is what I did. I used mri_convert on the relevant nii files, 
but I was wondering what to do with the surfaces files.
I thought it'll be easier to create all of these files directly in RAS 
orientation.

Thanks,
Noam

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Friday, March 8, 2019 11:05 PM
To: Freesurfer support list 
Cc: Sophie Esterer 
Subject: Re: [Freesurfer] recon-all: making sure that brain.mgz will be in RAS 
orientation.

Hi Noam

if you want your outputs in a specific coordinate system, why not just run 
recon-all, then mri_conver to whatever orientation you want? 
Internally we have a consistent orientation that you can't easily change

cheers
Bruce
On
Sat, 9 Mar 2019, Peled, Noam wrote:

> Dear group,
> I ran recon-all on a T1 nii file, which is in LAS orientation. The 
> brain.mgz turn out to be in LIA orientation.
> I've tried to convert the nii file to RAS (mri_convert 
> --in_orientation LAS --out_orientation RAS ...), and rerun recon-all, but it 
> didn't change the results.
> How do I make sure my output files will be in RAS orientation?
> 
> Thanks,
> Noam
> 
>

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[Freesurfer] applyMorph on talairach.m3z

[Peled, Noam]

Dear group,
How can I apply the talairach.m3z transformation on a list of points?
I was trying to use applyMorph on one of my subjects:
applyMorph --template $SUBJECTS_DIR/M1/mri/orig.mgz --transform 
$SUBJECTS_DIR/M1/mri/transforms/talairach.m3z point_list 
$SUBJECTS_DIR/M1/electrodes/electrodes_to_morph.txt tal.txt a

but I got this error:

Template name:/autofs/space/thibault_001/users/npeled/subjects//M1/mri/orig.mgz
After loading template
Template name:/autofs/space/thibault_001/users/npeled/subjects//M1/mri/orig.mgz
After loading template
 extension = m3z
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Abort (core dumped)

I'm using the FreeSurfer dev version (in martinos), and my SUBJECT_DIR is 
/autofs/space/thibault_001/users/npeled/subjects/
Thanks!
Noam
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[Freesurfer] mri_pretess: Cannot allocate memory

[Peled, Noam]

Dear group,
When trying to run mri_pretess, I'm getting this error:
znzTAGskip: tag=809120822, failed to calloc 1802706944 bytes!

Cannot allocate memory

Here is the full command I'm using (in the Martinos center, using ver6 stable):

mri_pretess /autofs/space/thibault_001/users/npeled/subjects/mg27/mri/aseg.mgz 
54 /autofs/space/thibault_001/users/npeled/subjects/mg27/mri/norm.mgz 
/autofs/space/thibault_001/users/npeled/subjects/mg27/tmp/274f23/54_filled.mgz

Thanks!
Noam



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[Freesurfer] recon-all and fMRI coordinates mismatch

[Peled, Noam]

Hello,
After running recon-all on a patient, the resulting T1.mgz coordinates system 
turned to be LIA. Can I guarantee the recon-all output will be in RAS?
I also would like to run FS-FAST on this patient's fMRI task dataset, which is 
in LSA.
Any recommendation what should I do to make sure both are in the same 
coordinates system (I preferred RAS)?

Thanks,
Noam
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Re: [Freesurfer] recon-all and fMRI coordinates mismatch

[Peled, Noam]

Thanks Doug!
Good to know that.
I realized I had a problem when I got activation on the wrong side (right 
finger tapping shows activation on the right hemisphere)
The analysis was done in another hospital when I just helped them remotely. 
They told me that their analysis software shows the activation is in the other 
hemisphere.

Any idea why something like that can happen?
Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Monday, May 4, 2020 1:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch

The actual orientation of the input should not matter as long as the nominal 
orientation matches the true orientation -- FS automatically handles the 
orientation correctly. When you ask whether the output will be "in RAS", are 
you asking whether the left side is truly the left (and right is right)? If so, 
the answer is yes.
On 5/4/2020 12:50 PM, Peled, Noam wrote:
Hello,
After running recon-all on a patient, the resulting T1.mgz coordinates system 
turned to be LIA. Can I guarantee the recon-all output will be in RAS?
I also would like to run FS-FAST on this patient's fMRI task dataset, which is 
in LSA.
Any recommendation what should I do to make sure both are in the same 
coordinates system (I preferred RAS)?

Thanks,
Noam



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Re: [Freesurfer] recon-all and fMRI coordinates mismatch

[Peled, Noam]

We are running a pilot, to try to analyze their epileptic monitoring unit 
datasets using the Martinos tools (FreeSurfer and MNE)
The analysis was on an fMRI nii file, which I checked before running fsFast, 
and it was LSA.
I wouldn't suspect anything is wrong unless I knew how the results should look 
like

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Monday, May 4, 2020 1:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch

I'd need a lot more details. Where they using FreeSurfer? Sometimes the data 
will go through several conversions and formats before analysis. If the 
orientation info was lost or changed, then that could explain it
On 5/4/2020 1:22 PM, Peled, Noam wrote:
Thanks Doug!
Good to know that.
I realized I had a problem when I got activation on the wrong side (right 
finger tapping shows activation on the right hemisphere)
The analysis was done in another hospital when I just helped them remotely. 
They told me that their analysis software shows the activation is in the other 
hemisphere.

Any idea why something like that can happen?
Thanks,
Noam

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: Monday, May 4, 2020 1:03 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch

The actual orientation of the input should not matter as long as the nominal 
orientation matches the true orientation -- FS automatically handles the 
orientation correctly. When you ask whether the output will be "in RAS", are 
you asking whether the left side is truly the left (and right is right)? If so, 
the answer is yes.
On 5/4/2020 12:50 PM, Peled, Noam wrote:
Hello,
After running recon-all on a patient, the resulting T1.mgz coordinates system 
turned to be LIA. Can I guarantee the recon-all output will be in RAS?
I also would like to run FS-FAST on this patient's fMRI task dataset, which is 
in LSA.
Any recommendation what should I do to make sure both are in the same 
coordinates system (I preferred RAS)?

Thanks,
Noam




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Re: [Freesurfer] recon-all and fMRI coordinates mismatch

[Peled, Noam]

They are using dcm2niix of MRIcroGL


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Monday, May 4, 2020 2:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch

How was the nii created? Ie, how did it go from dicom to nii?
On 5/4/2020 1:56 PM, Peled, Noam wrote:
We are running a pilot, to try to analyze their epileptic monitoring unit 
datasets using the Martinos tools (FreeSurfer and MNE)
The analysis was on an fMRI nii file, which I checked before running fsFast, 
and it was LSA.
I wouldn't suspect anything is wrong unless I knew how the results should look 
like

Thanks,
Noam

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: Monday, May 4, 2020 1:48 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch

I'd need a lot more details. Where they using FreeSurfer? Sometimes the data 
will go through several conversions and formats before analysis. If the 
orientation info was lost or changed, then that could explain it
On 5/4/2020 1:22 PM, Peled, Noam wrote:
Thanks Doug!
Good to know that.
I realized I had a problem when I got activation on the wrong side (right 
finger tapping shows activation on the right hemisphere)
The analysis was done in another hospital when I just helped them remotely. 
They told me that their analysis software shows the activation is in the other 
hemisphere.

Any idea why something like that can happen?
Thanks,
Noam

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: Monday, May 4, 2020 1:03 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch

The actual orientation of the input should not matter as long as the nominal 
orientation matches the true orientation -- FS automatically handles the 
orientation correctly. When you ask whether the output will be "in RAS", are 
you asking whether the left side is truly the left (and right is right)? If so, 
the answer is yes.
On 5/4/2020 12:50 PM, Peled, Noam wrote:
Hello,
After running recon-all on a patient, the resulting T1.mgz coordinates system 
turned to be LIA. Can I guarantee the recon-all output will be in RAS?
I also would like to run FS-FAST on this patient's fMRI task dataset, which is 
in LSA.
Any recommendation what should I do to make sure both are in the same 
coordinates system (I preferred RAS)?

Thanks,
Noam





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Re: [Freesurfer] recon-all and fMRI coordinates mismatch

[Peled, Noam]

I think the latest one, but maybe it'll a good idea to start with the original 
dicoms and not with the nii.

Thanks!
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Monday, May 4, 2020 4:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch

I have used that before and it seems to work. What version are you/they using? 
I remember this kind of problem years ago when FSFAST was using SPM to 
initialize the registration; at some point SPM changed the interpretation of 
the coordinates which caused a left-right reversal.
On 5/4/2020 3:25 PM, Peled, Noam wrote:
They are using dcm2niix of MRIcroGL


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: Monday, May 4, 2020 2:11 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch

How was the nii created? Ie, how did it go from dicom to nii?
On 5/4/2020 1:56 PM, Peled, Noam wrote:
We are running a pilot, to try to analyze their epileptic monitoring unit 
datasets using the Martinos tools (FreeSurfer and MNE)
The analysis was on an fMRI nii file, which I checked before running fsFast, 
and it was LSA.
I wouldn't suspect anything is wrong unless I knew how the results should look 
like

Thanks,
Noam

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: Monday, May 4, 2020 1:48 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch

I'd need a lot more details. Where they using FreeSurfer? Sometimes the data 
will go through several conversions and formats before analysis. If the 
orientation info was lost or changed, then that could explain it
On 5/4/2020 1:22 PM, Peled, Noam wrote:
Thanks Doug!
Good to know that.
I realized I had a problem when I got activation on the wrong side (right 
finger tapping shows activation on the right hemisphere)
The analysis was done in another hospital when I just helped them remotely. 
They told me that their analysis software shows the activation is in the other 
hemisphere.

Any idea why something like that can happen?
Thanks,
Noam

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: Monday, May 4, 2020 1:03 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all and fMRI coordinates mismatch

The actual orientation of the input should not matter as long as the nominal 
orientation matches the true orientation -- FS automatically handles the 
orientation correctly. When you ask whether the output will be "in RAS", are 
you asking whether the left side is truly the left (and right is right)? If so, 
the answer is yes.
On 5/4/2020 12:50 PM, Peled, Noam wrote:
Hello,
After running recon-all on a patient, the resulting T1.mgz coordinates system 
turned to be LIA. Can I guarantee the recon-all output will be in RAS?
I also would like to run FS-FAST on this patient's fMRI task dataset, which is 
in LSA.
Any recommendation what should I do to make sure both are in the same 
coordinates system (I preferred RAS)?

Thanks,
Noam






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[Freesurfer] preproc-sess error with FreeSurfer 7.1

[Peled, Noam]

Dear FreeSurfer experts!
We are running FsFast pipeline to analysis our language task for epilepsy 
patients.
Usually we are using FreeSurfer 5.3. We want to use a newer version, so I 
decided to jump right to 7.1 (dev)
When trying to run
preproc-sess -surface {trg_subject} lhrh -s {subject} -fwhm {fwhm} -fsd {fsd} 
-mni305 -per-run -stc siemens
I got the following error:

mri_info --nslices --o 
/autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/tmp.110620/nslices.dat
 
/autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/fmcpr.nii.gz
nslices =  44
slicedelay --nslices 44 --siemens --o 
/autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/tmp.110620/sdf.txt
 --ngroups 1
  File "/usr/local/freesurfer/dev/bin/slicedelay", line 9
print "USAGE: slicedelay --help";
   ^
SyntaxError: Missing parentheses in call to 'print'

When I reran the same pipeline with FreeSurfer 5.3, it seems to work.
Is it a bug in 7.1? Or should we change something in the call?

Thanks,
Noam
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Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

[Peled, Noam]

Thanks!
I’m only working with python3, so I prefer to set python to call python3 and 
not python2.
Is there an option to set the python bin file name used by FreeSurfer 
(/usr/bin/python2.7 for example)?

Thanks,
Noam

From: fsbuild 
Sent: Thursday, October 29, 2020 9:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Peled, Noam 
Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1


External Email - Use Caution
Hello Noam,

The python script /usr/local/freesurfer/dev/bin/slicedelay needs to be run with 
a version of python that is 2.X, i.e.,

$ file /usr/local/freesurfer/dev/bin/slicedelay
/usr/local/freesurfer/dev/bin/slicedelay: Python script, ASCII text executable


$ which python2
/bin/python2
$ python2 /usr/local/freesurfer/dev/bin/slicedelay --help
USAGE: slicedelay --help
  --o slicedelayfile
  --nslices nslices : total number of slices in the volume
  --order order (up,down,odd,even,siemens)
  --ngroups ngroups (number of slice groups for SMS)

Creates an FSL custom slice delay file for use with slicetimer 
(--tcustom=sdfile).
It has a single column of values, one for each slice. Each value is the slice 
delay
measured as a fraction of the TR and range from +0.5 (beginning of the TR) to
-0.5 (end of the TR). Used for slice-time correction of fMRI.

$ which python3
/space/freesurfer/python/linux/bin/python3
$ python3 /usr/local/freesurfer/dev/bin/slicedelay --help
  File "/usr/local/freesurfer/dev/bin/slicedelay", line 9
print "USAGE: slicedelay --help";
   ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("USAGE: 
slicedelay --help")?


So I think that means that for you,
$ which python
- is going to return a python from your PATH such that typing the command 
“python —version” will report it is rev 3.X and not 2.X.

You can try setting the PATH environment variable such that the first python 
program found in PATH reports it is version 2.X.

- R.


On Oct 29, 2020, at 20:47, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:

/usr/local/freesurfer/dev/bin/slicedelay

​
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Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

[Peled, Noam]

-rwxrwxr-x 1 rd521 rd521 4951 Oct 30 04:45 
/usr/local/freesurfer/dev/bin/slicedelay

Thanks!

From: Greve, Douglas N.,Ph.D. 
Sent: Friday, October 30, 2020 10:38 AM
To: Peled, Noam ; Freesurfer support list 

Cc: Gumenyuk, Valentina ; Stufflebeam, Steven M. 
; Douglas N Greve 
Subject: Re: preproc-sess error with FreeSurfer 7.1

can you send the result of
ls -l `which  slicedelay`

On 10/29/2020 8:47 PM, Peled, Noam wrote:
Dear FreeSurfer experts!
We are running FsFast pipeline to analysis our language task for epilepsy 
patients.
Usually we are using FreeSurfer 5.3. We want to use a newer version, so I 
decided to jump right to 7.1 (dev)
When trying to run
preproc-sess -surface {trg_subject} lhrh -s {subject} -fwhm {fwhm} -fsd {fsd} 
-mni305 -per-run -stc siemens
I got the following error:

mri_info --nslices --o 
/autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/tmp.110620/nslices.dat
 
/autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/fmcpr.nii.gz
nslices =  44
slicedelay --nslices 44 --siemens --o 
/autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/tmp.110620/sdf.txt
 --ngroups 1
  File "/usr/local/freesurfer/dev/bin/slicedelay", line 9
print "USAGE: slicedelay --help";
   ^
SyntaxError: Missing parentheses in call to 'print'

When I reran the same pipeline with FreeSurfer 5.3, it seems to work.
Is it a bug in 7.1? Or should we change something in the call?

Thanks,
Noam

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Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

[Peled, Noam]

Thanks,
In my system, I aliased the python command to a local anaconda python3.8.
So to be able to use slicedelay, should I first alias python to python2?

Thanks,
Noam

From: fsbuild 
Sent: Friday, October 30, 2020 2:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Peled, Noam 
Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1


External Email - Use Caution
Please keep in mind that the system python installed on both CentOS6 and 
CentOS7 (/usr/bin/python) is python 2.X, so scripts aren’t expecting to run a 
version 3 via the “python” interpreter found in a standard system PATH.  As far 
as I know only 1 python interpreter can be returned thru PATH (whichever python 
it finds first according to the order of the entries in PATH).

But you can alias python to be something different in your shell, e.g., here 
using csh,

% alias python python3
… or alias to whatever python rev 3 you want to run.

If your PATH is set to return system 2.X version, e.g., /usr/bin/python., then 
any script like slicedeleay should still find /usr/bin/python thru PATH.  But 
typing python at the terminal will run whatever the alias points to.  The which 
command will show you this (CentOS7),

% which python
/usr/bin/python
% python --version
Python 2.7.5
% alias python python3
% python  --version
Python 3.6.8
% which python
python:aliased to python3
% /usr/local/freesurfer/dev/bin/slicedelay --help
USAGE: slicedelay --help
  --o slicedelayfile
  --nslices nslices : total number of slices in the volume
  --order order (up,down,odd,even,siemens)
  --ngroups ngroups (number of slice groups for SMS)
< … rest of output deleted …>
% unalias python
% which python
/usr/bin/python



- R.


On Oct 29, 2020, at 21:46, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:

Thanks!
I’m only working with python3, so I prefer to set python to call python3 and 
not python2.
Is there an option to set the python bin file name used by FreeSurfer 
(/usr/bin/python2.7 for example)?

Thanks,
Noam

From: fsbuild mailto:fsbu...@contbay.com>>
Sent: Thursday, October 29, 2020 9:33 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: Peled, Noam mailto:npe...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1

External Email - Use Caution
Hello Noam,

The python script /usr/local/freesurfer/dev/bin/slicedelay needs to be run with 
a version of python that is 2.X, i.e.,

$ file /usr/local/freesurfer/dev/bin/slicedelay
/usr/local/freesurfer/dev/bin/slicedelay: Python script, ASCII text executable

$ which python2
/bin/python2
$ python2 /usr/local/freesurfer/dev/bin/slicedelay --help
USAGE: slicedelay --help
  --o slicedelayfile
  --nslices nslices : total number of slices in the volume
  --order order (up,down,odd,even,siemens)
  --ngroups ngroups (number of slice groups for SMS)

Creates an FSL custom slice delay file for use with slicetimer 
(--tcustom=sdfile).
It has a single column of values, one for each slice. Each value is the slice 
delay
measured as a fraction of the TR and range from +0.5 (beginning of the TR) to
-0.5 (end of the TR). Used for slice-time correction of fMRI.

$ which python3
/space/freesurfer/python/linux/bin/python3
$ python3 /usr/local/freesurfer/dev/bin/slicedelay --help
  File "/usr/local/freesurfer/dev/bin/slicedelay", line 9
print "USAGE: slicedelay --help";
   ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("USAGE: 
slicedelay --help")?

So I think that means that for you,
$ which python
- is going to return a python from your PATH such that typing the command 
“python —version” will report it is rev 3.X and not 2.X.

You can try setting the PATH environment variable such that the first python 
program found in PATH reports it is version 2.X.

- R.

On Oct 29, 2020, at 20:47, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:

/usr/local/freesurfer/dev/bin/slicedelay

​
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[Freesurfer] error: MatrixMultiply: m1 is null

[Peled, Noam]

Dear FreeSurfer community,
I encountered a recon-all error where I couldn't find on the web.
The error message is: "error: MatrixMultiply: m1 is null!". You can find the 
complete log attached.
I used the stable7.1.1 version.

Thanks,
Noam


recon-all.log
Description: recon-all.log
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Re: [Freesurfer] error: MatrixMultiply: m1 is null

[Peled, Noam]

Thanks Andrew!
Yes, it seems like something is really wrong with this scan:
/autofs/space/frieda_003/users/valia/epilepsy_clin/5545419_1449/3D/dicom/IM-0001-0001.dcm

I’ll try to find another sequence.
Thanks!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Hoopes, Andrew
Sent: Tuesday, November 24, 2020 11:14 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] error: MatrixMultiply: m1 is null

Hi Noam,

Do the volumes look okay? I’m seeing a lot of ‘non-orthogonal axes’ warnings in 
the log. If that’s not the issue, this could be a bug that’s randomly occurring 
with parallel recons in v7. Although, I’ve never seen it fail during 
mri_convert. Can you try to rerun? It might succeed the second time. If not, 
can you send us the input scan and try again without the -parallel flag.

best
Andrew

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Peled, Noam" 
mailto:npe...@mgh.harvard.edu>>
Reply-To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, November 24, 2020 at 10:10 PM
To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] error: MatrixMultiply: m1 is null

Dear FreeSurfer community,
I encountered a recon-all error where I couldn’t find on the web.
The error message is: “error: MatrixMultiply: m1 is null!”. You can find the 
complete log attached.
I used the stable7.1.1 version.

Thanks,
Noam
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[Freesurfer] Saving more than one figure using freeview

[Peled, Noam]

Hello all,
Can I use the -ss flag in freeview to save more than one figure?
Currently, I'm calling freeiew 3 times, each time with a different viewport 
(sagittal, coronal, and axial)

Thanks,
Noam

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Re: [Freesurfer] Saving more than one figure using freeview

[Peled, Noam]

That’s great!
Thanks Ruopeng!
Should I also add the -noquit flag in each line:

freeview foo.mgz -viewport x -ss pic1.jpg -noquit
-viewport y -ss pic2.jpg -noquit
-viewport z -ss pic3.jpg -noquit

Thanks!
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wang, Ruopeng
Sent: Tuesday, January 26, 2021 4:59 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Saving more than one figure using freeview

Hi Noam,

You can’t save multiple figures with one -ss flag. If you want to save multiple 
screenshots without having to load the volume every time, you can write a 
series of command lines in a text file like this:

freeview foo.mgz -viewport x -ss pic1.jpg
-viewport y -ss pic2.jpg
-viewport z -ss pic3.jpg

Then run:
freeview -cmd foo.txt

Ruopeng


On Jan 26, 2021, at 1:18 PM, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:

Hello all,
Can I use the -ss flag in freeview to save more than one figure?
Currently, I’m calling freeiew 3 times, each time with a different viewport 
(sagittal, coronal, and axial)

Thanks,
Noam

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[Freesurfer] recon-all transformations: raw nii to T1.mgz

[Peled, Noam]

Hello,
I was running recon-all on a raw T1 image with the following properties:
dimensions: 126 x 144 x 88
voxel sizes: 1.78, 1.78, 1.78
Orientation: PSL

Besides the raw T1, I have other nii files with the same dimensions and 
orientation that I want to visualize on top of the recon-all output T1.mgz.
How can I run the same transformations (and reslicing) that were used in 
recon-all (from my raw nii file to T1.mgz) on the other nii files?

Thanks!
Noam
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[Freesurfer] Registering preop and postop MRI scans

[Peled, Noam]

Dear group,
I have preop and postop MRI scans of an epileptic patient.
I ran recon-all on the preop, and bbregister on the postop to register it to 
the preop.
I'm not sure why, but the results weren't really good.
Maybe I should try using the longitudinal pipeline?

Thanks,
Noam
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Re: [Freesurfer] Registering preop and postop MRI scans

[Peled, Noam]

After running the longitudinal pipeline, it's still not registered well.
Doug, I don't think I should attach the figures here, but you take a look at 
the registration here:
freeview mg150.long.mg150_base/mri/T1.mgz 
mg150_postop.long.mg150_base/mri/T1.mgz
Where the folders are in 
/autofs/space/mmvtclin_001/thibault/1/users/npeled/subjects

Thanks!
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Monday, May 10, 2021 12:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Registering preop and postop MRI scans

Can you be more specific that "weren't really good"?
On 5/6/2021 12:03 PM, Peled, Noam wrote:
Dear group,
I have preop and postop MRI scans of an epileptic patient.
I ran recon-all on the preop, and bbregister on the postop to register it to 
the preop.
I'm not sure why, but the results weren't really good.
Maybe I should try using the longitudinal pipeline?

Thanks,
Noam



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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

[Peled, Noam]

Hello!

I'm trying to use freeview to visualize FSPGR  dicoms files.

I'm using ubuntu 18.04 with tcsh shell. I'm getting the following error:

sh: 1: Syntax error: Bad fd number



Here is the full error message:



Starting DICOMRead2()

dcmfile =~/Desktop/04254335/05641194

dcmdir = ~/Desktop/04254335

Ref Series No = 3

Found 200 files, checking for dicoms

Found 200 files, checking for dicoms

5

/05641194

Found 198 dicom files in series.

Found 198 dicom files in series.

oms

5

/05641194

First Sorting

Computing Slice Direction

Vs: 0 0 1

Vs: 0 0 1

Second Sorting

IsDWI = 0, IsPhilipsDWI = 0

Counting frames

nframes = 1

nslices = 198

ndcmfiles = 198

INFO: rescale not needed

PE Dir = ROW (dicom read)

Loading pixel data

JPEG compressed, decompressing

cd ~/Desktop

fsdcmdecompress --i ~/Desktop/04254335/05641194 --o 
/tmp/basuia.tmp.decompressed.dcm.yK9HZZ --jpeg >& 
/tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out

sh: 1: Syntax error: Bad fd number

ERROR: 512, see /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out for more 
details

QObject::~QObject: Timers cannot be stopped from another thread

Thanks,
Noam
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The information in this e-mail is intended only for the person to whom it is 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

[Peled, Noam]

The same error.
Also, when trying to run recon-all on these files.

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wang, Ruopeng
Sent: Wednesday, September 1, 2021 12:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

What if you use mri_convert to convert them to a mgz or nii volume? Do you get 
the same error?

Ruopeng


On Sep 1, 2021, at 10:52 AM, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:

Hello!
I’m trying to use freeview to visualize FSPGR  dicoms files.
I’m using ubuntu 18.04 with tcsh shell. I’m getting the following error:
sh: 1: Syntax error: Bad fd number

Here is the full error message:

Starting DICOMRead2()
dcmfile =~/Desktop/04254335/05641194
dcmdir = ~/Desktop/04254335
Ref Series No = 3
Found 200 files, checking for dicoms
Found 200 files, checking for dicoms
5
/05641194
Found 198 dicom files in series.
Found 198 dicom files in series.
oms
5
/05641194
First Sorting
Computing Slice Direction
Vs: 0 0 1
Vs: 0 0 1
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 198
ndcmfiles = 198
INFO: rescale not needed
PE Dir = ROW (dicom read)
Loading pixel data
JPEG compressed, decompressing
cd ~/Desktop
fsdcmdecompress --i ~/Desktop/04254335/05641194 --o 
/tmp/basuia.tmp.decompressed.dcm.yK9HZZ --jpeg >& 
/tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out
sh: 1: Syntax error: Bad fd number
ERROR: 512, see /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out for more 
details
QObject::~QObject: Timers cannot be stopped from another thread

Thanks,
Noam
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The information in this e-mail is intended only for the person to whom it is 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

[Peled, Noam]

Unfortunately, it’s patient data from another hospital, and I also can’t access 
the files.
I’m just helping them to use FreeSurfer.
Is there a debug version that outputs more information? The temp file 
(basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg) is empty.

Thanks!
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wang, Ruopeng
Sent: Thursday, September 2, 2021 10:00 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

Would it be possible to send me the dicom files?

Ruopeng


On Sep 1, 2021, at 1:14 PM, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:

The same error.
Also, when trying to run recon-all on these files.

Thanks,
Noam

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wang, Ruopeng
Sent: Wednesday, September 1, 2021 12:57 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

What if you use mri_convert to convert them to a mgz or nii volume? Do you get 
the same error?

Ruopeng



On Sep 1, 2021, at 10:52 AM, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:

Hello!
I’m trying to use freeview to visualize FSPGR  dicoms files.
I’m using ubuntu 18.04 with tcsh shell. I’m getting the following error:
sh: 1: Syntax error: Bad fd number

Here is the full error message:

Starting DICOMRead2()
dcmfile =~/Desktop/04254335/05641194
dcmdir = ~/Desktop/04254335
Ref Series No = 3
Found 200 files, checking for dicoms
Found 200 files, checking for dicoms
5
/05641194
Found 198 dicom files in series.
Found 198 dicom files in series.
oms
5
/05641194
First Sorting
Computing Slice Direction
Vs: 0 0 1
Vs: 0 0 1
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 198
ndcmfiles = 198
INFO: rescale not needed
PE Dir = ROW (dicom read)
Loading pixel data
JPEG compressed, decompressing
cd ~/Desktop
fsdcmdecompress --i ~/Desktop/04254335/05641194 --o 
/tmp/basuia.tmp.decompressed.dcm.yK9HZZ --jpeg >& 
/tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out
sh: 1: Syntax error: Bad fd number
ERROR: 512, see /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out for more 
details
QObject::~QObject: Timers cannot be stopped from another thread

Thanks,
Noam
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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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

[Peled, Noam]

Yes! Thanks!
dmc2niix did the trick.
I wonder why mri_convert failed.

Thanks!
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fischl, Bruce
Sent: Thursday, September 2, 2021 12:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

Hi Noam

can you convert them with any dicom converter to any other format? dcm2nii? 
That kind of thing?
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 Peled, Noam 
mailto:npe...@mgh.harvard.edu>>
Sent: Thursday, September 2, 2021 12:19 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number


Unfortunately, it's patient data from another hospital, and I also can't access 
the files.

I'm just helping them to use FreeSurfer.

Is there a debug version that outputs more information? The temp file 
(basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg) is empty.



Thanks!

Noam



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wang, Ruopeng
Sent: Thursday, September 2, 2021 10:00 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number



Would it be possible to send me the dicom files?



Ruopeng



On Sep 1, 2021, at 1:14 PM, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:



The same error.

Also, when trying to run recon-all on these files.



Thanks,

Noam



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wang, Ruopeng
Sent: Wednesday, September 1, 2021 12:57 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number



What if you use mri_convert to convert them to a mgz or nii volume? Do you get 
the same error?



Ruopeng



On Sep 1, 2021, at 10:52 AM, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:



Hello!

I'm trying to use freeview to visualize FSPGR  dicoms files.

I'm using ubuntu 18.04 with tcsh shell. I'm getting the following error:

sh: 1: Syntax error: Bad fd number



Here is the full error message:



Starting DICOMRead2()

dcmfile =~/Desktop/04254335/05641194

dcmdir = ~/Desktop/04254335

Ref Series No = 3

Found 200 files, checking for dicoms

Found 200 files, checking for dicoms

5

/05641194

Found 198 dicom files in series.

Found 198 dicom files in series.

oms

5

/05641194

First Sorting

Computing Slice Direction

Vs: 0 0 1

Vs: 0 0 1

Second Sorting

IsDWI = 0, IsPhilipsDWI = 0

Counting frames

nframes = 1

nslices = 198

ndcmfiles = 198

INFO: rescale not needed

PE Dir = ROW (dicom read)

Loading pixel data

JPEG compressed, decompressing

cd ~/Desktop

fsdcmdecompress --i ~/Desktop/04254335/05641194 --o 
/tmp/basuia.tmp.decompressed.dcm.yK9HZZ --jpeg >& 
/tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out

sh: 1: Syntax error: Bad fd number

ERROR: 512, see /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out for more 
details

QObject::~QObject: Timers cannot be stopped from another thread



Thanks,

Noam

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Freesurfer@nmr.mgh.harvard.edu
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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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

[Peled, Noam]

Great! Thanks!!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Tuesday, September 7, 2021 9:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

yes, in the process now of upgrading. We'll use dcm2niix internally.
On 9/7/2021 5:11 PM, Fischl, Bruce wrote:
Our dicom reader is probably too old
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 Peled, Noam
Sent: Tuesday, September 7, 2021 2:56 PM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

Yes! Thanks!
dmc2niix did the trick.
I wonder why mri_convert failed.

Thanks!
Noam

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fischl, Bruce
Sent: Thursday, September 2, 2021 12:44 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

Hi Noam

can you convert them with any dicom converter to any other format? dcm2nii? 
That kind of thing?
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 Peled, Noam 
mailto:npe...@mgh.harvard.edu>>
Sent: Thursday, September 2, 2021 12:19 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number


Unfortunately, it's patient data from another hospital, and I also can't access 
the files.

I'm just helping them to use FreeSurfer.

Is there a debug version that outputs more information? The temp file 
(basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg) is empty.



Thanks!

Noam



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wang, Ruopeng
Sent: Thursday, September 2, 2021 10:00 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number



Would it be possible to send me the dicom files?



Ruopeng



On Sep 1, 2021, at 1:14 PM, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:



The same error.

Also, when trying to run recon-all on these files.



Thanks,

Noam



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wang, Ruopeng
Sent: Wednesday, September 1, 2021 12:57 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number



What if you use mri_convert to convert them to a mgz or nii volume? Do you get 
the same error?



Ruopeng



On Sep 1, 2021, at 10:52 AM, Peled, Noam 
mailto:npe...@mgh.harvard.edu>> wrote:



Hello!

I'm trying to use freeview to visualize FSPGR  dicoms files.

I'm using ubuntu 18.04 with tcsh shell. I'm getting the following error:

sh: 1: Syntax error: Bad fd number



Here is the full error message:



Starting DICOMRead2()

dcmfile =~/Desktop/04254335/05641194

dcmdir = ~/Desktop/04254335

Ref Series No = 3

Found 200 files, checking for dicoms

Found 200 files, checking for dicoms

5

/05641194

Found 198 dicom files in series.

Found 198 dicom files in series.

oms

5

/05641194

First Sorting

Computing Slice Direction

Vs: 0 0 1

Vs: 0 0 1

Second Sorting

IsDWI = 0, IsPhilipsDWI = 0

Counting frames

nframes = 1

nslices = 198

ndcmfiles = 198

INFO: rescale not needed

PE Dir = ROW (dicom read)

Loading pixel data

JPEG compressed, decompressing

cd ~/Desktop

fsdcmdecompress --i ~/Desktop/04254335/05641194 --o 
/tmp/basuia.tmp.decompressed.dcm.yK9HZZ --jpeg >& 
/tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out

sh: 1: Syntax error: Bad fd number

ERROR: 512, see /tmp/basuia.tmp.decompressed.dcm.yK9HZZ.dcmdjpeg.out for more 
details

QObject::~QObject: Timers cannot be stopped from another thread



Thanks,

Noam

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Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

[Peled, Noam]

Thanks Doug!
Unfortunately, removing the parallel flag didn’t help:

“ …
After retessellation of defect 43 (v0=79551), euler #=-51 
(145804,431777,285922) : difference with theory (-68) = -17
CORRECTING DEFECT 44 (vertices=9236, convex hull=4698, v0=79649)
Command terminated by signal 11
@#@FSTIME  2021:11:17:14:54:07 mris_fix_topology N 14 e 12788.52 S 1.14 U 
12786.35 P 99% M 1761016 F 0 R 581366 W 0 c 79248 w 3 I 0 O 3960 L 1.01 1.00 
1.00
@#@FSLOADPOST 2021:11:17:18:27:16 mris_fix_topology N 14 1.00 1.00 1.00
“

Any ideas?
Thanks again,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Wednesday, November 17, 2021 10:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

I'm not sure what is happening. Does it work without the parallel flag?
btw, you are not using 7.2
here's your build: build-stamp.txt: 
freesurfer-linux-ubuntu18_x86_64-dev-20210824-e101185

On 11/16/2021 4:26 PM, Peled, Noam wrote:

Dear Freesurfer group,

I was running recon-all (Freesurfer 7.2 on Ubuntu) and received the following 
error:



“

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig 
orig.nofix -out orig.premesh -ga -seed 1234 UC07 rh



Waiting for PID 6337 of (6337 6340) to complete...

Waiting for PID 6340 of (6337 6340) to complete...

/home/basuia/Documents/mmvt_root/freesurfer/bin/reconbatchjobs: line 77:  6340 
Segmentation fault  (core dumped) exec $JOB >> $LOG 2>&1

PIDs (6337 6340) completed and logs appended.

“



Please find the log file attached.

Any idea what is the problem?



Thanks,

Noam



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Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

[Peled, Noam]

Hey Bruce,
I’m helping a group from University of Cincinnati with this patient, so 
unfortunately I don’t have access to the data.
They are running recon-all on a laptop that has 32 GB of RAM. Nothing else big 
is running in the background.
Would you recommend manually fixing the defect in the skull?

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fischl, Bruce
Sent: Thursday, November 18, 2021 9:29 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

Hi Noam

How much ram do you have in the machine? Is anything else big running? You can 
also examine that defect and see what is going on. 9000 vertices is pretty big 
so something significant like a chunk of skull might be fixable

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 Peled, Noam
Sent: Thursday, November 18, 2021 9:05 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

Thanks Doug!
Unfortunately, removing the parallel flag didn’t help:

“ …
After retessellation of defect 43 (v0=79551), euler #=-51 
(145804,431777,285922) : difference with theory (-68) = -17
CORRECTING DEFECT 44 (vertices=9236, convex hull=4698, v0=79649)
Command terminated by signal 11
@#@FSTIME  2021:11:17:14:54:07 mris_fix_topology N 14 e 12788.52 S 1.14 U 
12786.35 P 99% M 1761016 F 0 R 581366 W 0 c 79248 w 3 I 0 O 3960 L 1.01 1.00 
1.00
@#@FSLOADPOST 2021:11:17:18:27:16 mris_fix_topology N 14 1.00 1.00 1.00
“

Any ideas?
Thanks again,
Noam

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: Wednesday, November 17, 2021 10:09 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault

I'm not sure what is happening. Does it work without the parallel flag?
btw, you are not using 7.2
here's your build: build-stamp.txt: 
freesurfer-linux-ubuntu18_x86_64-dev-20210824-e101185
On 11/16/2021 4:26 PM, Peled, Noam wrote:

Dear Freesurfer group,

I was running recon-all (Freesurfer 7.2 on Ubuntu) and received the following 
error:



“

 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig 
orig.nofix -out orig.premesh -ga -seed 1234 UC07 rh



Waiting for PID 6337 of (6337 6340) to complete...

Waiting for PID 6340 of (6337 6340) to complete...

/home/basuia/Documents/mmvt_root/freesurfer/bin/reconbatchjobs: line 77:  6340 
Segmentation fault  (core dumped) exec $JOB >> $LOG 2>&1

PIDs (6337 6340) completed and logs appended.

“



Please find the log file attached.

Any idea what is the problem?



Thanks,

Noam


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Re: [Freesurfer] recon-all: error in creating rh.white.H

[Peled, Noam]

Thanks, Tim,
The lh.white.K and lh.white.H were created.

Thanks,
Noam

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Tim Schäfer
Sent: Friday, January 14, 2022 11:18 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all: error in creating rh.white.H

External Email - Use Caution

Can you check whether any of the .H/.K files were created? They contain the 
per-vertex mean/Gaussian curvature for the respective surface, but what's more 
important is that they are symbolic links.

If you try to save recon-all output onto a drive formatted with a file system 
that does not support symbolic links (e.g., a shared network drive from a 
Windows file server), the files cannot be created, leading to that error. Could 
that be the case?

Best,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy 
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

> On 01/14/2022 5:02 PM Peled, Noam  wrote:
> 
>  
> Dear group
> A colleague of mine was trying to run recon-all on one of her patients and 
> received an error message.
> After looking at the attached log, I'm not sure what is the source of the 
> problem.
> The T1 looks quite good.
> She is using freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b
> 
> Thanks!
> Noam
> 
> From: Gumenyuk, Valentina 
> Sent: Friday, January 14, 2022 10:48 AM
> To: Peled, Noam 
> Subject: UNMC error
> 
> 
> External Email - Use Caution
> freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b
> 
> 
> Thanks!
> -Valia
> 
> The information in this e-mail may be privileged and confidential, intended 
> only for the use of the addressee(s) above. Any unauthorized use or 
> disclosure of this information is prohibited. If you have received this 
> e-mail by mistake, please delete it and immediately contact the sender.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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> ILb6t3CkavMjWW_nxwyyxu1PN1TgscB4QZ-FytHeSqusptpTywRWLdz_UesUhERZ2HIf9b
> L5hfdwcdkxDCN6nk3G2WGPfUe5b4BqrPtwnpBtDa68vhEU9dAA3zR3NL0EHuX9l1Vu0G7u
> kg4U4DsnOQCtsMVkLpl9kh-2KLVWMzqMbCS35tNLuuidP_2MLx-JsjGIKlvTVS4nQQRho-
> _KkEoZw95d89dU2R7x1uqPPqVr8qn6RI2BuY6jBIbPfjf2Hms-gHBVxq4dDVWf658Kn_D5
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> n%2Flistinfo%2Ffreesurfer 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 Mass General Brigham Compliance HelpLine at 
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>  . 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.
> Please note that this e-mail is not secure (encrypted).  If you do not wish 
> to continue communication over unencrypted e-mail, please notify the sender 
> of this message immediately.  Continuing to send or respond to e-mail after 
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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 Mass General Brigham 
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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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] The fsaverage link points to an older freesurfer version

[Peled, Noam]

Hello,
I was running recon-all where SUBJECTS_DIR is 
/space/megraid/clinical/MEG-MRI/seder/freesurfer, where we store our patient's 
Freesurfer reconstructions.
I received the following error:
ERROR: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage!
   The fsaverage link probably points to an older freesurfer version

Indeed, the fsaverage link points to version 6, where we are using 7.1.1
I think it makes sense to change it, but I don't have the permission to do that 
( the owner is zkaufman, and the group is fsbuild)

Thanks,
Noam

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Re: [Freesurfer] Neverending mris_fix_topology

[Peled, Noam]

Thanks Bruce, I'm going to try that now.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Fischl, Bruce
Sent: Thursday, February 24, 2022 1:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Neverending mris_fix_topology

Hi Noam

Have you tried running it without -parallel? It looks like it is waiting for 
some other PID to finish
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 Peled, Noam
Sent: Thursday, February 24, 2022 12:36 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Neverending mris_fix_topology

Dear group,
I'm trying to run recon-all 
(freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) on my Martinos' 
desktop.
I killed it after waiting quite a of time for the mris_fix_topology to be 
completed:
Waiting for PID 225967 of (225964 225967) to complete...
What can I do to be able to process this subject?
I attached the recon-all log. You can also find all the logs here:
/autofs/space/mmvtclin_001/thibault/1/users/npeled/subjects/UN07/scripts

Thanks!
Noam
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Re: [Freesurfer] Neverending mris_fix_topology

[Peled, Noam]

It's running quite a long time, with this repeating message:
"
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
"
I think the cerebellum and the dura seem to be ok:
[cid:image001.png@01D82A5B.F7813420]

Any ideas?
Thanks!
Noam


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam
Sent: Thursday, February 24, 2022 1:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Neverending mris_fix_topology

Thanks Bruce, I'm going to try that now.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Fischl, Bruce
Sent: Thursday, February 24, 2022 1:05 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Neverending mris_fix_topology

Hi Noam

Have you tried running it without -parallel? It looks like it is waiting for 
some other PID to finish
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 Peled, Noam
Sent: Thursday, February 24, 2022 12:36 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Neverending mris_fix_topology

Dear group,
I'm trying to run recon-all 
(freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) on my Martinos' 
desktop.
I killed it after waiting quite a of time for the mris_fix_topology to be 
completed:
Waiting for PID 225967 of (225964 225967) to complete...
What can I do to be able to process this subject?
I attached the recon-all log. You can also find all the logs here:
/autofs/space/mmvtclin_001/thibault/1/users/npeled/subjects/UN07/scripts

Thanks!
Noam
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[Freesurfer] Create an lta or xfm file for mri_vol2vol

[Peled, Noam,PhD]

Dear group,
I have 2 images (preop t1 and postop CT), and a 4x4 registration matrix (as a 
text file).
Is there an easy way to create an lta or xfm file to use it with mri_vol2vol?


Thanks!
Noam

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contains patient information, please contact the Mass General Brigham 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] recon-all cannot execute: required file not found

[Peled, Noam,PhD]

Dear group,
I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)
I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)
After sourcing Freesurfer, recon-all gives following error:
.../freesurfer/bin/recon-all: cannot execute: required file not found

Other functions, e.g. freeview, mri_info, all seem to work as expected

Would love some help.
Thanks,
Noam


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Re: [Freesurfer] recon-all cannot execute: required file not found

[Peled, Noam,PhD]

Thanks Yujing,
Yes, I looked for the file permissions using ls -l. It does have execute 
permissions.
I also tried running chmod which didn't help.

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found


After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.



1. ‘ls -l $FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the 
execute permissions?

2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the permission





Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all cannot execute: required file not found



Dear group,

I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)

I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)

After sourcing Freesurfer, recon-all gives following error:

.../freesurfer/bin/recon-all: cannot execute: required file not found



Other functions, e.g. freeview, mri_info, all seem to work as expected



Would love some help.

Thanks,

Noam




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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] recon-all cannot execute: required file not found

[Peled, Noam,PhD]

I'm just trying now to run the "recon-all -version", also without any arguments.
Both produce the same error.

Thanks!
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 19, 2024 3:10 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found


I’m wondering how you ran recon-all.  Do you see the error even running it w/o 
any arguments?



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:59 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found



Thanks Yujing,

Yes, I looked for the file permissions using ls -l. It does have execute 
permissions.

I also tried running chmod which didn't help.



Thanks,

Noam



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found



After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.



1. ‘ls -l $FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the 
execute permissions?

2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the permission





Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] recon-all cannot execute: required file not found



Dear group,

I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)

I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)

After sourcing Freesurfer, recon-all gives following error:

.../freesurfer/bin/recon-all: cannot execute: required file not found



Other functions, e.g. freeview, mri_info, all seem to work as expected



Would love some help.

Thanks,

Noam




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