[Freesurfer] Order of recommended reconstructions - CPs and skullstripping

[Thomas Fink]

Dear experts,

In the recommended reconstructions (
http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction) it is
stated that one should do CPs first and than do skullstripping.
Why is that?

However the recon-all after CPs (recon-all -autorecon2-cp -autorecon3
-subjid) includes less (or later) stages from the autorecon process (only
stages 12-31) than the recon-all after skullstripping (recon-all
-autorecon2 -autorecon3 -subjid) (stages 6-31) does.
Wouldn't this indicate that skullstripping should be done before applying
CPs?

Best regards
Thomas
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[Freesurfer] Some beginner questions on cortical thickness analyses

[Tudor Popescu]

Dear all,

I have some questions I could not find an answer to myself, I'd really
appreciate it if anyone could help out.

1) How should recon-all be used to process all subjects' data (i.e. obtain
the surface for each subject) before taking it to QDEC (or command prompt)
for a group thickness analysis? The QDEC tutorial mentions a separate
tutorial for the recon-all preprocessing part, but it is not at all clear
which one that is. Is there more to it than just typing "recon-all --i
file.nii –i  file.dcm –subject bert –all" for each subject (assuming NIFTI
structurals)?

2) Is mri_glmfit FreeSurfer's equivalent of the randomise command in FSL,
i.e. it does nonparametric permutation-based inference based on the given
design matrix and produces statistical maps? Or are there differences
between the two in how the GLM is applied?

3) Freeview and tksurfer seem to overlap in scope - when would you use one
rather than the other? Does it have to do with viewing structurals vs
statistically-generated maps?

4) I see that points on reconall-generated surfaces are always referred to
in tutorials as vertices rather than voxels. Since both represent the "unit
of space", what exactly is the difference between them?

Many thanks in advance!
Tudor
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[Freesurfer] Error from mri_concat while using QDEC

[Tudor Popescu]

Hello everyone,

I tried doing the QDEC group analysis tutorial, however after doing
everything as instructed in the tutorial, when pressing Analyze I get the
error message:

*Error in Analyze: command failed: mri_concat
/media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh
/media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh
(..)*

..even though those files are all accessible there! I pasted that same
mri_concat manually into the terminal, however no output is produced at the
command prompt, nor any files are created.

In previous attempts, I used to also get this error

*" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in
SUBJECTS_DIR "*
*Syntax error: Bad fd number"*

after following the sh/bash workaround from this
previous
thread, I no longer get that error, however get stuck with the error
mentioned above.

My SUBJECTS_DIR already contains a copy of the default subjects folder.

Debug info below. Any help greatly appreciated!
Tudor

 freesurfer-Linux-centos4-stable-pub-v5.1.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /home/virtualuser/freesurfer
FSFAST_HOME   /home/virtualuser/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /media/Dell/_FS/buckner_data/subjects
MNI_DIR   /home/virtualuser/freesurfer/mni
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[Freesurfer] mri_cc segfault

[Pedro Paulo de Magalhães Oliveira Junior]

I'm having a segfault with mri_cc it's happening sometimes using FreeSurfer
5.1

Searching the mailing list I saw a similar problem in 2008 but with no
answers.

The relevant portion of recon-all.log:

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta
c70eb728-c505-46c2-a2a1-1ed409c36ea1

will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as
/usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta
reading aseg from
/usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/aseg.auto_noCCseg.mgz
reading norm from
/usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/norm.mgz
2358 voxels in left wm, 13846 in right wm, xrange [122, 136]
searching rotation angles z=[-10  4], y=[-31 -17]
^Msearching scale 1 Z rot -9.8  ^Msearching scale 1 Z rot -9.5  ^Msearching
scale 1 Z rot -9.3  ^Msearching scale 1 Z rot -9.0  ^Msearching scale 1 Z
rot -8.8  ^Msearching scale 1 Z rot -8.5  ^Msearching scale 1 Z rot -8.3
 ^Msearching scale 1 Z rot -8.0  ^Msearching scale 1 Z rot -7.8
 ^Msearching scale 1 Z rot -7.5  ^Msearching scale 1 Z rot -7.3
 ^Msearching scale 1 Z rot -7.0  ^Msearching scale 1 Z rot -6.8
 ^Msearching scale 1 Z rot -6.5  ^Msearching scale 1 Z rot -6.3
 ^Msearching scale 1 Z rot -6.0  ^Msearching scale 1 Z rot -5.8
 ^Msearching scale 1 Z rot -5.5  ^Msearching scale 1 Z rot -5.3
 ^Msearching scale 1 Z rot -5.0  ^Msearching scale 1 Z rot -4.8
 ^Msearching scale 1 Z rot -4.5  ^Msearching scale 1 Z rot -4.3
 ^Msearching scale 1 Z rot -4.0  ^Msearching scale 1 Z rot -3.8
 ^Msearching scale 1 Z rot -3.5  ^Msearching scale 1 Z rot -3.3
 ^Msearching scale 1 Z rot -3.0  ^Msearching scale 1 Z rot -2.8
 ^Msearching scale 1 Z rot -2.5  ^Msearching scale 1 Z rot -2.3
 ^Msearching scale 1 Z rot -2.0  ^Msearching scale 1 Z rot -1.8
^Msearching scale 1 Z rot -1.5  ^Msearching scale 1 Z rot -1.3  ^Msearching
scale 1 Z rot -1.0  ^Msearching scale 1 Z rot -0.8  ^Msearching scale 1 Z
rot -0.5  ^Msearching scale 1 Z rot -0.3  ^Msearching scale 1 Z rot -0.0
 ^Msearching scale 1 Z rot 0.2  ^Msearching scale 1 Z rot 0.5  ^Msearching
scale 1 Z rot 0.7  ^Msearching scale 1 Z rot 1.0  ^Msearching scale 1 Z rot
1.2  ^Msearching scale 1 Z rot 1.5  ^Msearching scale 1 Z rot 1.7
 ^Msearching scale 1 Z rot 2.0  ^Msearching scale 1 Z rot 2.2  ^Msearching
scale 1 Z rot 2.5  ^Msearching scale 1 Z rot 2.7  ^Msearching scale 1 Z rot
3.0  ^Msearching scale 1 Z rot 3.2  ^Msearching scale 1 Z rot 3.5
 ^Msearching scale 1 Z rot 3.7  global minimum found at slice 129.0,
rotations (-2.52, -3.27)
final transformation (x=129.0, yr=-2.521, zr=-3.273):
 0.997   0.057  -0.044  -2.975;
-0.057   0.998   0.003  -6.742;
 0.044  -0.000   0.999  -9.547;
 0.000   0.000   0.000   1.000;
Segmentation fault

Thanks

PPJ
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
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[Freesurfer] Info change size nii

[Andrea Tateo]

Hello FS experts,

I have a problem to solve.

I have a binary image.nii to estimate the segmentation of freesurfer.

His size is 70,30,70 but format nii includes other information: resolution, 
origin, ...
so, when I convert image.nii to image.mgz, I see an image of size256, 256, 256, 
(256 slides for orientation).

I need to have the image.nii of size 256,256,256 voxels.

there is a FreeSurfer's command which allows me to convert to image.nii with 
size 256 256 256

(if I convert image.nii to image.mgz, the image.mgz has size 256, 256,256)

Thank you very much

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[Freesurfer] space of T1.mgz

[Mojdeh Zamyadi]

Hi all,

I want to segment the hippocampus into head/body/tail in itk SNAP using 
the hippocampus mask that I create from the result of recon-all 
segmentation. My question is, are the T1.mgz and aseg.mgz files in the 
native space of the image or in the atlas space? I know the voxel size 
is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45), 
but I want to know if the original images are registered to a common 
atlas space or just resampled to a different voxel size. The reason I'm 
asking this, is because I'm doing a group study and I want to make sure 
all my subjects are in the same space so that the segmentation I do is 
accurate for all.

Thanks for your help,

Mojdeh Zamyadi, MSc
Clinical Research Project Assistant
The Hospital for Sick Children
555 University Avenue
Toronto ON M5G 1X8


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[Freesurfer] "nu_estimate_np_and_em" error during recon-all

[Tudor Popescu]

Hello,

First of all, apologies for asking for help three times today! THings will
hopefully become clearer once I get used to FS a bit; I really do
appreciate the amazing support provided by the team behind FreeSurfer!

I ran the following command on one of my structurals:

*recon-all -subject M01 -i M01.nii.gz -all*

After a few minutes, recon-all ended with the following message:

*Assertion failed at line 827 in file templates/CachedArray.cc*
*nu_estimate_np_and_em: crashed while running volume_stats (termination
status=256)*
*nu_correct: crashed while running nu_estimate_np_and_em (termination
status=256)*
*ERROR: nu_correct*
*Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
2009 i686 GNU/Linux*

I apologise for reporting an error that's already been reported in the
past, but unfortunately the solutions suggested in those past threads did
not work in my case. To address a few of them:

   - my PATH (listed below) does not seem to include two MNI installations
   *
   
/home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
   *
   - the version of FreeSurfer that I installed is the latest disk image
   available on the website
   (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did not see
   any dev version that would presumably include any missing libraries
   presumably implied by the above error
   - I tried updating the Xubuntu inside my VirtualBox, however it reports
   an insufficient space problem that from I can see does not have a trivial
   fix

Advance thanks for any help!
Tudor
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[Freesurfer] vertices out of range after mris_label2annot

[Linda Douw]

Hi experts,

I have a bunch of custom-made labels (from the ConnectomeMapper software)
that I want to put into a single annotation file. Therefore, I create a
color-lookup table and use mris_label2annot as follows:

mris_label2annot --s fsaveragec --h lh --ctab lh_laus500_clut_new.txt --a
laus500_fixed_newest  --l $LABEL_DIR/lh.bankssts_1.label --l
$LABEL_DIR/lh.bankssts_2.label --l $LABEL_DIR/lh.bankssts_3.label ... etc
for all labels

Then, I try to load this annotation with tksurfer, but some errors come up
(see below). What do these error messages mean? Could it have something to
do with some vertices not having a label assigned to them?
The annotation does look okay on tksurfer, but I run into problems later
when using it, so I do need to work out why these errors come up.

Thanks,
Linda

tksurfer fsaveragec lh inflated -annotation laus500_fixed_newest
subject is fsaveragec
hemiis lh
surface is inflated
surfer: current subjects dir: /cluster/neuromind/douw/scans/controls
surfer: in dir with "scripts" in name
surfer: session root data dir ($session) set to:
surfer: /autofs/cluster/neuromind/douw
checking for nofix files in 'inflated'
Reading image info (/cluster/neuromind/douw/scans/controls/fsaveragec)
Reading /cluster/neuromind/douw/scans/controls/fsaveragec/mri/orig.mgz
surfer: Reading header info from
/cluster/neuromind/douw/scans/controls/fsaveragec/mri/orig.mgz
surfer: vertices=163842, faces=327680
reading colortable from annotation file...
colortable with 502 entries read (originally
/cluster/neuromind/douw/scans/lh_laus500_clut_new.txt)
Found embedded color table in annotation.
Warning: vertex 206 with annotation 100e251 - out of range!
Warning: vertex 1280 with annotation 100e251 - out of range!
Warning: vertex 2371 with annotation 100e251 - out of range!
Warning: vertex 2372 with annotation 100e251 - out of range!
Warning: vertex 5282 with annotation 100e251 - out of range!
Warning: vertex 5283 with annotation 100e251 - out of range!
Warning: vertex 5284 with annotation 100e251 - out of range!
Warning: vertex 5285 with annotation 100e251 - out of range!
Warning: vertex 6914 with annotation 100e251 - out of range!
Warning: vertex 6915 with annotation 100e251 - out of range!
Warning: vertex 9669 with annotation 100e251 - out of range!
Warning: vertex 9670 with annotation 100e251 - out of range!
Warning: vertex 9671 with annotation 100e251 - out of range!
Warning: vertex 9672 with annotation 100e251 - out of range!
Warning: vertex 9673 with annotation 100e251 - out of range!
Warning: vertex 11176 with annotation 100e251 - out of range!
Warning: vertex 11178 with annotation 100e251 - out of range!
Warning: vertex 12962 with annotation 100e251 - out of range!
Warning: vertex 12963 with annotation 100e251 - out of range!
Warning: vertex 12964 with annotation 100e251 - out of range!
Warning: vertex 12965 with annotation 100e251 - out of range!
Warning: vertex 15365 with annotation 100e251 - out of range!
Warning: vertex 21604 with annotation 100e251 - out of range!
Warning: vertex 21605 with annotation 100e251 - out of range!
Warning: vertex 21606 with annotation 100e251 - out of range!
Warning: vertex 21607 with annotation 100e251 - out of range!
Warning: vertex 21608 with annotation 100e251 - out of range!
Warning: vertex 21609 with annotation 100e251 - out of range!
Warning: vertex 21610 with annotation 100e251 - out of range!
Warning: vertex 21611 with annotation 100e251 - out of range!
Warning: vertex 21612 with annotation 100e251 - out of range!
Warning: vertex 21613 with annotation 100e251 - out of range!
Warning: vertex 21614 with annotation 100e251 - out of range!
Warning: vertex 21615 with annotation 100e251 - out of range!
Warning: vertex 21616 with annotation 100e251 - out of range!
Warning: vertex 21617 with annotation 100e251 - out of range!
Warning: vertex 21618 with annotation 100e251 - out of range!
Warning: vertex 27939 with annotation 100e251 - out of range!
Warning: vertex 27940 with annotation 100e251 - out of range!
Warning: vertex 27941 with annotation 100e251 - out of range!
Warning: vertex 27942 with annotation 100e251 - out of range!
Warning: vertex 27943 with annotation 100e251 - out of range!
Warning: vertex 27944 with annotation 100e251 - out of range!
Warning: vertex 27945 with annotation 100e251 - out of range!
Warning: vertex 27946 with annotation 100e251 - out of range!
Warning: vertex 27947 with annotation 100e251 - out of range!
Warning: vertex 28990 with annotation 100e251 - out of range!
Warning: vertex 28991 with annotation 100e251 - out of range!
Warning: vertex 31491 with annotation 100e251 - out of range!
Warning: vertex 31493 with annotation 100e251 - out of range!
Warning: vertex 31494 with annotation 100e251 - out of range!
Warning: vertex 31495 with annotation 100e251 - out of range!
Warning: vertex 31496 with annotation 100e251 - out of range!
Warning: vertex 31497 with annotation 100e251 - out of range!
Warning: vertex 39242 with annotation 100e

Re: [Freesurfer] volume of interest

[Douglas N Greve]

If you load the volume in with MRIread
a = MRIread('yourvolume.mgz');
a.vox2ras1 is the one-based vox2ras matrix which takes a 1-based column, 
row, slice and converts it to RAS. So you just need to convert your 
indices to col, row, slice and apply this matrix.

doug


On 12/17/2012 06:53 PM, octavian lie wrote:
> Dear Douglas,
>
> Thank you very much for your input.
>
> 1. I generated the ind matrix as per your script, but what I wanted is 
> to get a matrix with the RAS coordinates for the pixels indexed in 
> ind. Is there a way to do this?
>
> Thank you,
>
> Octavian

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

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

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Re: [Freesurfer] Some beginner questions on cortical thickness analyses

[Douglas N Greve]

On 12/18/2012 06:48 AM, Tudor Popescu wrote:
> Dear all,
>
> I have some questions I could not find an answer to myself, I'd really 
> appreciate it if anyone could help out.
>
> 1) How should recon-all be used to process all subjects' data (i.e. 
> obtain the surface for each subject) before taking it to QDEC (or 
> command prompt) for a group thickness analysis? The QDEC tutorial 
> mentions a separate tutorial for the recon-all preprocessing part, but 
> it is not at all clear which one that is. Is there more to it than 
> just typing "recon-all --i file.nii –i file.dcm –subject bert –all" 
> for each subject (assuming NIFTI structurals)?
To have it run through to the end, that is all you need (note that if 
file.nii and file.dcm represent the same volume, then only pass one). 
You will need to visually inspect and possibly manually fix your data. 
That is what the trouble shooting tutorial is about.
>
> 2) Is mri_glmfit FreeSurfer's equivalent of the randomise command in 
> FSL, i.e. it does nonparametric permutation-based inference based on 
> the given design matrix and produces statistical maps? Or are there 
> differences between the two in how the GLM is applied?
mri_glmfit just performs the GLM analysis, ie, given an input y and a 
design matrix X and contrast matrices C1, C2, etc, it will fit the model 
to the data, compue beta's and residual variances, and test the 
contrasts, and computes parametric statistics. mri_glmfit-sim computes 
stats based on permutation or simulation stats.
>
> 3) Freeview and tksurfer seem to overlap in scope - when would you use 
> one rather than the other? Does it have to do with viewing structurals 
> vs statistically-generated maps?
They do overlap a lot and there is on one case where you would use one 
over the other. freeview is newer, and tksurfer will eventually be 
phased out.
>
> 4) I see that points on reconall-generated surfaces are always 
> referred to in tutorials as vertices rather than voxels. Since both 
> represent the "unit of space", what exactly is the difference between 
> them?
Conceptually, not much. "Vertex" is a term commonly used in mesh models 
in which the distance between the vertices is not fixed. "Voxels" comes 
from imaging. Really, they just represent different communities.

doug
>
> Many thanks in advance!
> Tudor
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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Re: [Freesurfer] Error from mri_concat while using QDEC

[Douglas N Greve]

Hi Tudor,
Can you run mri_concat from the command line with the --debug option 
first. Send us the FULL command line and the full terminal output.
doug



On 12/18/2012 09:35 AM, Tudor Popescu wrote:
> Hello everyone,
>
> I tried doing the QDEC group analysis tutorial, however after doing 
> everything as instructed in the tutorial, when pressing Analyze I get 
> the error message:
>
> /Error in Analyze: command failed: mri_concat 
> /media/Dell/_FS/buckner_data/subjects/140/surf/lh.thickness.fwhm10.fsaverage.mgh
>  
> /media/Dell/_FS/buckner_data/subjects/049/surf/lh.thickness.fwhm10.fsaverage.mgh
>  
> (..)/
>
> ..even though those files are all accessible there! I pasted that same 
> mri_concat manually into the terminal, however no output is produced 
> at the command prompt, nor any files are created.
>
> In previous attempts, I used to also get this error
>
> /" .ERROR: QdecProject::VerifySubjects: Couldn't find subject '032' in 
> SUBJECTS_DIR "/
> /Syntax error: Bad fd number"/
>
> after following the sh/bash workaround from this 
> previous
>  
> thread, I no longer get that error, however get stuck with the error 
> mentioned above.
>
> My SUBJECTS_DIR already contains a copy of the default subjects folder.
>
> Debug info below. Any help greatly appreciated!
> Tudor
>
>  freesurfer-Linux-centos4-stable-pub-v5.1.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /home/virtualuser/freesurfer
> FSFAST_HOME   /home/virtualuser/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /media/Dell/_FS/buckner_data/subjects
> MNI_DIR   /home/virtualuser/freesurfer/mni
>
>
>
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Re: [Freesurfer] space of T1.mgz

[Douglas N Greve]

Hi Mojdeh, try looking at this doc
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
doug

On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote:
> Hi all,
>
> I want to segment the hippocampus into head/body/tail in itk SNAP using
> the hippocampus mask that I create from the result of recon-all
> segmentation. My question is, are the T1.mgz and aseg.mgz files in the
> native space of the image or in the atlas space? I know the voxel size
> is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45),
> but I want to know if the original images are registered to a common
> atlas space or just resampled to a different voxel size. The reason I'm
> asking this, is because I'm doing a group study and I want to make sure
> all my subjects are in the same space so that the segmentation I do is
> accurate for all.
>
> Thanks for your help,
>
> Mojdeh Zamyadi, MSc
> Clinical Research Project Assistant
> The Hospital for Sick Children
> 555 University Avenue
> Toronto ON M5G 1X8
>
>
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>
>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Info change size nii

[Douglas N Greve]

Hi Andrea, sorry, I don't quite follow what your question is. If I 
understand correctly, you have an image that is 70,30,70 that you want 
to analyze in FreeSurfer? If that covers the whole head, then the voxel 
size is probably going to be to large to get good surfaces.
doug


On 12/18/2012 10:34 AM, Andrea Tateo wrote:
> Hello FS experts,
>
> I have a problem to solve.
>
> I have a binary image.nii to estimate the segmentation of freesurfer.
>
> His size is 70,30,70 but format nii includes other information: 
> resolution, origin, ...
> so, when I convert image.nii to image.mgz, I see an image of size256, 
> 256, 256, (256 slides for orientation).
>
> I need to have the image.nii of size 256,256,256 voxels.
>
> there is a FreeSurfer's command which allows me to convert to 
> image.nii with size 256 256 256
>
> (if I convert image.nii to image.mgz, the image.mgz has size 256, 256,256)
>
> Thank you very much
>
> Andrea
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] vertices out of range after mris_label2annot

[Douglas N Greve]

Hi Linda, check your color table to make sure that the entry indices are 
in numerical order without a gap (i,e 1 2 3 4 5 is ok, but 1 3 4 5 would 
not be).
doug


On 12/18/2012 11:49 AM, Linda Douw wrote:
> Hi experts,
>
> I have a bunch of custom-made labels (from the ConnectomeMapper software)
> that I want to put into a single annotation file. Therefore, I create a
> color-lookup table and use mris_label2annot as follows:
>
> mris_label2annot --s fsaveragec --h lh --ctab lh_laus500_clut_new.txt --a
> laus500_fixed_newest  --l $LABEL_DIR/lh.bankssts_1.label --l
> $LABEL_DIR/lh.bankssts_2.label --l $LABEL_DIR/lh.bankssts_3.label ... etc
> for all labels
>
> Then, I try to load this annotation with tksurfer, but some errors come up
> (see below). What do these error messages mean? Could it have something to
> do with some vertices not having a label assigned to them?
> The annotation does look okay on tksurfer, but I run into problems later
> when using it, so I do need to work out why these errors come up.
>
> Thanks,
> Linda
>
> tksurfer fsaveragec lh inflated -annotation laus500_fixed_newest
> subject is fsaveragec
> hemiis lh
> surface is inflated
> surfer: current subjects dir: /cluster/neuromind/douw/scans/controls
> surfer: in dir with "scripts" in name
> surfer: session root data dir ($session) set to:
> surfer: /autofs/cluster/neuromind/douw
> checking for nofix files in 'inflated'
> Reading image info (/cluster/neuromind/douw/scans/controls/fsaveragec)
> Reading /cluster/neuromind/douw/scans/controls/fsaveragec/mri/orig.mgz
> surfer: Reading header info from
> /cluster/neuromind/douw/scans/controls/fsaveragec/mri/orig.mgz
> surfer: vertices=163842, faces=327680
> reading colortable from annotation file...
> colortable with 502 entries read (originally
> /cluster/neuromind/douw/scans/lh_laus500_clut_new.txt)
> Found embedded color table in annotation.
> Warning: vertex 206 with annotation 100e251 - out of range!
> Warning: vertex 1280 with annotation 100e251 - out of range!
> Warning: vertex 2371 with annotation 100e251 - out of range!
> Warning: vertex 2372 with annotation 100e251 - out of range!
> Warning: vertex 5282 with annotation 100e251 - out of range!
> Warning: vertex 5283 with annotation 100e251 - out of range!
> Warning: vertex 5284 with annotation 100e251 - out of range!
> Warning: vertex 5285 with annotation 100e251 - out of range!
> Warning: vertex 6914 with annotation 100e251 - out of range!
> Warning: vertex 6915 with annotation 100e251 - out of range!
> Warning: vertex 9669 with annotation 100e251 - out of range!
> Warning: vertex 9670 with annotation 100e251 - out of range!
> Warning: vertex 9671 with annotation 100e251 - out of range!
> Warning: vertex 9672 with annotation 100e251 - out of range!
> Warning: vertex 9673 with annotation 100e251 - out of range!
> Warning: vertex 11176 with annotation 100e251 - out of range!
> Warning: vertex 11178 with annotation 100e251 - out of range!
> Warning: vertex 12962 with annotation 100e251 - out of range!
> Warning: vertex 12963 with annotation 100e251 - out of range!
> Warning: vertex 12964 with annotation 100e251 - out of range!
> Warning: vertex 12965 with annotation 100e251 - out of range!
> Warning: vertex 15365 with annotation 100e251 - out of range!
> Warning: vertex 21604 with annotation 100e251 - out of range!
> Warning: vertex 21605 with annotation 100e251 - out of range!
> Warning: vertex 21606 with annotation 100e251 - out of range!
> Warning: vertex 21607 with annotation 100e251 - out of range!
> Warning: vertex 21608 with annotation 100e251 - out of range!
> Warning: vertex 21609 with annotation 100e251 - out of range!
> Warning: vertex 21610 with annotation 100e251 - out of range!
> Warning: vertex 21611 with annotation 100e251 - out of range!
> Warning: vertex 21612 with annotation 100e251 - out of range!
> Warning: vertex 21613 with annotation 100e251 - out of range!
> Warning: vertex 21614 with annotation 100e251 - out of range!
> Warning: vertex 21615 with annotation 100e251 - out of range!
> Warning: vertex 21616 with annotation 100e251 - out of range!
> Warning: vertex 21617 with annotation 100e251 - out of range!
> Warning: vertex 21618 with annotation 100e251 - out of range!
> Warning: vertex 27939 with annotation 100e251 - out of range!
> Warning: vertex 27940 with annotation 100e251 - out of range!
> Warning: vertex 27941 with annotation 100e251 - out of range!
> Warning: vertex 27942 with annotation 100e251 - out of range!
> Warning: vertex 27943 with annotation 100e251 - out of range!
> Warning: vertex 27944 with annotation 100e251 - out of range!
> Warning: vertex 27945 with annotation 100e251 - out of range!
> Warning: vertex 27946 with annotation 100e251 - out of range!
> Warning: vertex 27947 with annotation 100e251 - out of range!
> Warning: vertex 28990 with annotation 100e251 - out of range!
> Warning: vertex 28991 with annotation 100e251 - out of range!
> Warning: vertex 31491 with annotation 1

Re: [Freesurfer] "nu_estimate_np_and_em" error during recon-all

[Douglas N Greve]

Can you send the recon-all.log file (located in the subject/scripts folder).
doug


On 12/18/2012 11:41 AM, Tudor Popescu wrote:
> Hello,
>
> First of all, apologies for asking for help three times today! THings 
> will hopefully become clearer once I get used to FS a bit; I really do 
> appreciate the amazing support provided by the team behind FreeSurfer!
>
> I ran the following command on one of my structurals:
>
> /recon-all -subject M01 -i M01.nii.gz -all/
>
> After a few minutes, recon-all ended with the following message:
>
> /Assertion failed at line 827 in file templates/CachedArray.cc/
> /nu_estimate_np_and_em: crashed while running volume_stats 
> (termination status=256)/
> /nu_correct: crashed while running nu_estimate_np_and_em (termination 
> status=256)/
> /ERROR: nu_correct/
> /Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 
> UTC 2009 i686 GNU/Linux/
>
> I apologise for reporting an error that's already been reported in the 
> past, but unfortunately the solutions suggested in those past threads 
> did not work in my case. To address a few of them:
>
>   * my PATH (listed below) does not seem to include two MNI installations
> 
> //home/virtualuser/freesurfer/bin:/home/virtualuser/freesurfer/fsfast/bin:/home/virtualuser/freesurfer/tktools:/home/virtualuser/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games/
>   * the version of FreeSurfer that I installed is the latest disk
> image available on the website
> (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full) - I did
> not see any dev version that would presumably include any missing
> libraries presumably implied by the above error
>   * I tried updating the Xubuntu inside my VirtualBox, however it
> reports an insufficient space problem that from I can see does not
> have a trivial fix
>
> Advance thanks for any help!
> Tudor
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] volume of interest

[Douglas N Greve]

Use the matlab ind2sub command
doug


On 12/18/2012 12:38 PM, octavian lie wrote:
> Dear Douglas,
>
>
> How do I convert the index to its CRS correspondent?
> I could think of using in matlab something like
> ind=c+r*255+s* 255^2
> then using floor () to obtain c,r,s, but seems convoluted, is there 
> any code written on this that you can share?
> Thank you again,
>
> Octavian.
>
>
>
> On Tue, Dec 18, 2012 at 11:06 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> If you load the volume in with MRIread
> a = MRIread('yourvolume.mgz');
> a.vox2ras1 is the one-based vox2ras matrix which takes a 1-based
> column, row, slice and converts it to RAS. So you just need to
> convert your indices to col, row, slice and apply this matrix.
>
> doug
>
>
>
> On 12/17/2012 06:53 PM, octavian lie wrote:
>
> Dear Douglas,
>
> Thank you very much for your input.
>
> 1. I generated the ind matrix as per your script, but what I
> wanted is to get a matrix with the RAS coordinates for the
> pixels indexed in ind. Is there a way to do this?
>
> Thank you,
>
> Octavian
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> 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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> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
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>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] space of T1.mgz

[Mojdeh Zamyadi]

Hi Doug,

Thanks for the quick reply. I actually saw this link before first 
posting my question but it doesn't quite answer my question. What I want 
to know is whether the T1.mgz & aseg.mgz files are in an atlas space? if 
that's the case, it means the segmentation for all my subjects are in 
the same space and I don't need to convert anything if I want to compare 
their hippocampal volumes. I'm not quite sure if any sort of 
registration to an atlas is done in any steps of recon-all or not. I 
would appreciate if could clarify this for me.

Thanks,
-Mojdeh

On 12/18/2012 12:18 PM, Douglas N Greve wrote:
> Hi Mojdeh, try looking at this doc
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
> doug
>
> On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote:
>> Hi all,
>>
>> I want to segment the hippocampus into head/body/tail in itk SNAP using
>> the hippocampus mask that I create from the result of recon-all
>> segmentation. My question is, are the T1.mgz and aseg.mgz files in the
>> native space of the image or in the atlas space? I know the voxel size
>> is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45),
>> but I want to know if the original images are registered to a common
>> atlas space or just resampled to a different voxel size. The reason I'm
>> asking this, is because I'm doing a group study and I want to make sure
>> all my subjects are in the same space so that the segmentation I do is
>> accurate for all.
>>
>> Thanks for your help,
>>
>> Mojdeh Zamyadi, MSc
>> Clinical Research Project Assistant
>> The Hospital for Sick Children
>> 555 University Avenue
>> Toronto ON M5G 1X8
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>

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Re: [Freesurfer] space of T1.mgz

[Bruce Fischl]

Hi Mojdeh

they are not in atlas space and the volumes are for that subject, so you 
shouldn't have to do anything if I understand you correctly

cheers
Bruce

On Tue, 18 Dec 2012, Mojdeh Zamyadi wrote:

> Hi Doug,
>
> Thanks for the quick reply. I actually saw this link before first
> posting my question but it doesn't quite answer my question. What I want
> to know is whether the T1.mgz & aseg.mgz files are in an atlas space? if
> that's the case, it means the segmentation for all my subjects are in
> the same space and I don't need to convert anything if I want to compare
> their hippocampal volumes. I'm not quite sure if any sort of
> registration to an atlas is done in any steps of recon-all or not. I
> would appreciate if could clarify this for me.
>
> Thanks,
> -Mojdeh
>
> On 12/18/2012 12:18 PM, Douglas N Greve wrote:
>> Hi Mojdeh, try looking at this doc
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
>> doug
>>
>> On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote:
>>> Hi all,
>>>
>>> I want to segment the hippocampus into head/body/tail in itk SNAP using
>>> the hippocampus mask that I create from the result of recon-all
>>> segmentation. My question is, are the T1.mgz and aseg.mgz files in the
>>> native space of the image or in the atlas space? I know the voxel size
>>> is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45),
>>> but I want to know if the original images are registered to a common
>>> atlas space or just resampled to a different voxel size. The reason I'm
>>> asking this, is because I'm doing a group study and I want to make sure
>>> all my subjects are in the same space so that the segmentation I do is
>>> accurate for all.
>>>
>>> Thanks for your help,
>>>
>>> Mojdeh Zamyadi, MSc
>>> Clinical Research Project Assistant
>>> The Hospital for Sick Children
>>> 555 University Avenue
>>> Toronto ON M5G 1X8
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>
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>
>
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Re: [Freesurfer] space of T1.mgz

[Douglas N Greve]

No, they are not in any atlas space. The space is "native" in that 1mm 
in the image represents 1mm in the subject's brain. Therefore, you can 
directly compare the hippo volume across subjects.
doug

On 12/18/2012 12:59 PM, Mojdeh Zamyadi wrote:
> Hi Doug,
>
> Thanks for the quick reply. I actually saw this link before first 
> posting my question but it doesn't quite answer my question. What I 
> want to know is whether the T1.mgz & aseg.mgz files are in an atlas 
> space? if that's the case, it means the segmentation for all my 
> subjects are in the same space and I don't need to convert anything if 
> I want to compare their hippocampal volumes. I'm not quite sure if any 
> sort of registration to an atlas is done in any steps of recon-all or 
> not. I would appreciate if could clarify this for me.
>
> Thanks,
> -Mojdeh
>
> On 12/18/2012 12:18 PM, Douglas N Greve wrote:
>> Hi Mojdeh, try looking at this doc
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
>> doug
>>
>> On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote:
>>> Hi all,
>>>
>>> I want to segment the hippocampus into head/body/tail in itk SNAP using
>>> the hippocampus mask that I create from the result of recon-all
>>> segmentation. My question is, are the T1.mgz and aseg.mgz files in the
>>> native space of the image or in the atlas space? I know the voxel size
>>> is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45),
>>> but I want to know if the original images are registered to a common
>>> atlas space or just resampled to a different voxel size. The reason I'm
>>> asking this, is because I'm doing a group study and I want to make sure
>>> all my subjects are in the same space so that the segmentation I do is
>>> accurate for all.
>>>
>>> Thanks for your help,
>>>
>>> Mojdeh Zamyadi, MSc
>>> Clinical Research Project Assistant
>>> The Hospital for Sick Children
>>> 555 University Avenue
>>> Toronto ON M5G 1X8
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] volume of interest

[Douglas N Greve]

I don't know that function. vox2ras0 is used when you have 0-based 
indices (as in C) and vox2ras1 is used when  you have 1-based indices 
(as in matlab).
doug


On 12/18/2012 02:26 PM, octavian lie wrote:
> Can I use your function  xyzlab for this? If yes, I see that uses 
> vox2ras0 instead of vox2ras1. Please advise,
> Octavian
>
> On Tue, Dec 18, 2012 at 11:52 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Use the matlab ind2sub command
> doug
>
>
>
> On 12/18/2012 12:38 PM, octavian lie wrote:
>
> Dear Douglas,
>
>
> How do I convert the index to its CRS correspondent?
> I could think of using in matlab something like
> ind=c+r*255+s* 255^2
> then using floor () to obtain c,r,s, but seems convoluted, is
> there any code written on this that you can share?
> Thank you again,
>
> Octavian.
>
>
>
> On Tue, Dec 18, 2012 at 11:06 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>
> If you load the volume in with MRIread
> a = MRIread('yourvolume.mgz');
> a.vox2ras1 is the one-based vox2ras matrix which takes a
> 1-based
> column, row, slice and converts it to RAS. So you just need to
> convert your indices to col, row, slice and apply this matrix.
>
> doug
>
>
>
> On 12/17/2012 06:53 PM, octavian lie wrote:
>
> Dear Douglas,
>
> Thank you very much for your input.
>
> 1. I generated the ind matrix as per your script, but
> what I
> wanted is to get a matrix with the RAS coordinates for the
> pixels indexed in ind. Is there a way to do this?
>
> Thank you,
>
> Octavian
>
>
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
>  >
> Phone Number: 617-724-2358 
> >
> Fax: 617-726-7422   >
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> 
> FileDrop:
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> 
>
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
> The information in this e-mail is intended only for the
> person to
> whom it is
> addressed. If you believe this e-mail was sent to you in
> error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] Error in using tkregister2

[priyank]

Hi,
   I am using the command to check my registration and getting this 
error message: could not find orig as either mgz or COR. This is the 
command I am using.
   tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf
OUTPUT--
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume 18135.RS.mgz
reg file   18135_RS_register.dat
LoadVol1
ZeroCRAS   0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
 Input registration matrix 
-0.994  -0.040   0.100   2.799;
-0.097  -0.071  -0.993   2.262;
-0.047   0.997  -0.067   5.775;
  0.000   0.000   0.000   1.000;
float2int = 0
---
ERROR: could not find orig as either mgz or COR




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Re: [Freesurfer] Error in using tkregister2

[Bruce Fischl]

what is your SUBJECTS_DIR env variable?
On Tue, 18 Dec 2012, priyank wrote:

> Hi,
>   I am using the command to check my registration and getting this
> error message: could not find orig as either mgz or COR. This is the
> command I am using.
>   tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf
> OUTPUT--
> INFO: no target volume specified, assuming FreeSurfer orig volume.
> target  volume orig
> movable volume 18135.RS.mgz
> reg file   18135_RS_register.dat
> LoadVol1
> ZeroCRAS   0
> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
> Diagnostic Level -1
>  Input registration matrix 
> -0.994  -0.040   0.100   2.799;
> -0.097  -0.071  -0.993   2.262;
> -0.047   0.997  -0.067   5.775;
>  0.000   0.000   0.000   1.000;
> float2int = 0
> ---
> ERROR: could not find orig as either mgz or COR
> 
>
>
>
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>
>
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Re: [Freesurfer] Error in using tkregister2

[priyank]

I have these files in the folder 18135.
18135.RS.mgz   18135_RS_register.dat.log 18135_RS_register.dat.sum
18135.RS+orig.BRIK 18135_RS_register.dat.log.old 18135.RS.template.mgz
18135.RS+orig.HEAD 18135_RS_register.dat.mincost
18135_RS_register.dat  18135_RS_register.dat.param

and other freesurfer files in the folder 18135_FS (in the respective 
folders.. mri, surf...)...


I copied 18135.RS.mgz in the 18135_FS/mri/orig folder also.

I have tried both directories to be SUBJECTS_DIR but it didn't work.

Do I need to move all the files in 18135_FS/mri/orig folder?


On 12/18/2012 4:38 PM, Bruce Fischl wrote:

what is your SUBJECTS_DIR env variable?
On Tue, 18 Dec 2012, priyank wrote:


Hi,
  I am using the command to check my registration and getting this
error message: could not find orig as either mgz or COR. This is the
command I am using.
  tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf
OUTPUT-- 


INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume 18135.RS.mgz
reg file   18135_RS_register.dat
LoadVol1
ZeroCRAS   0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
 Input registration matrix 
-0.994  -0.040   0.100   2.799;
-0.097  -0.071  -0.993   2.262;
-0.047   0.997  -0.067   5.775;
 0.000   0.000   0.000   1.000;
float2int = 0
---
ERROR: could not find orig as either mgz or COR
 





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e-mail
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Re: [Freesurfer] Error in using tkregister2

[Bruce Fischl]

you don't need to move them. Where is the subject data that you ran 
recon-all on? You need to setenv SUBJECTS_DIR to point to that directory 
(the one that contains the subject you reconned)


cheers
Bruce


On Tue, 18 Dec 2012, 
priyank wrote:



I have these files in the folder 18135.
18135.RS.mgz   18135_RS_register.dat.log 18135_RS_register.dat.sum
18135.RS+orig.BRIK 18135_RS_register.dat.log.old 18135.RS.template.mgz
18135.RS+orig.HEAD 18135_RS_register.dat.mincost
18135_RS_register.dat  18135_RS_register.dat.param

and other freesurfer files in the folder 18135_FS (in the respective
folders.. mri, surf...)...

I copied 18135.RS.mgz in the 18135_FS/mri/orig folder also.

I have tried both directories to be SUBJECTS_DIR but it didn't work.

Do I need to move all the files in 18135_FS/mri/orig folder?


On 12/18/2012 4:38 PM, Bruce Fischl wrote:
  what is your SUBJECTS_DIR env variable?
  On Tue, 18 Dec 2012, priyank wrote:

Hi,
  I am using the command to check my
registration and getting this
error message: could not find orig as either mgz or
COR. This is the
command I am using.
  tkregister2 --mov 18135.RS.mgz --reg
18135_RS_register.dat --surf
OUTPUT-
-
INFO: no target volume specified, assuming
FreeSurfer orig volume.
target  volume orig
movable volume 18135.RS.mgz
reg file   18135_RS_register.dat
LoadVol    1
ZeroCRAS   0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16
greve Exp $
Diagnostic Level -1
 Input registration matrix 
-0.994  -0.040   0.100   2.799;
-0.097  -0.071  -0.993   2.262;
-0.047   0.997  -0.067   5.775;
 0.000   0.000   0.000   1.000;
float2int = 0
---
ERROR: could not find orig as either mgz or COR
---
-



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Re: [Freesurfer] Error in using tkregister2

[priyank]

Actually I received the reconned data. I did bbregistration: bbregister 
--s ${sub}_FS --mov $main_path/$sub/${sub}.RS.mgz --reg 
${sub}_RS_register.dat --init-fsl --bold --frame $framenum --nearest --o 
${sub}.RS.template.mgz

where $sub is subject id, which is 18135.

And now all the files are in 18135_FS. I only have resting state file in 
separate folder (18135).

On 12/18/2012 5:16 PM, Bruce Fischl wrote:
> you don't need to move them. Where is the subject data that you ran 
> recon-all on? You need to setenv SUBJECTS_DIR to point to that 
> directory (the one that contains the subject you reconned)
>
> cheers
> Bruce
>
>
> On Tue, 18 Dec 2012, priyank wrote:
>
>> I have these files in the folder 18135.
>> 18135.RS.mgz   18135_RS_register.dat.log 
>> 18135_RS_register.dat.sum
>> 18135.RS+orig.BRIK 18135_RS_register.dat.log.old 
>> 18135.RS.template.mgz
>> 18135.RS+orig.HEAD 18135_RS_register.dat.mincost
>> 18135_RS_register.dat  18135_RS_register.dat.param
>>
>> and other freesurfer files in the folder 18135_FS (in the respective
>> folders.. mri, surf...)...
>>
>> I copied 18135.RS.mgz in the 18135_FS/mri/orig folder also.
>>
>> I have tried both directories to be SUBJECTS_DIR but it didn't work.
>>
>> Do I need to move all the files in 18135_FS/mri/orig folder?
>>
>>
>> On 12/18/2012 4:38 PM, Bruce Fischl wrote:
>>   what is your SUBJECTS_DIR env variable?
>>   On Tue, 18 Dec 2012, priyank wrote:
>>
>> Hi,
>>   I am using the command to check my
>> registration and getting this
>> error message: could not find orig as either mgz or
>> COR. This is the
>> command I am using.
>>   tkregister2 --mov 18135.RS.mgz --reg
>> 18135_RS_register.dat --surf
>> OUTPUT- 
>>
>> -
>> INFO: no target volume specified, assuming
>> FreeSurfer orig volume.
>> target  volume orig
>> movable volume 18135.RS.mgz
>> reg file   18135_RS_register.dat
>> LoadVol1
>> ZeroCRAS   0
>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16
>> greve Exp $
>> Diagnostic Level -1
>>  Input registration matrix 
>> -0.994  -0.040   0.100   2.799;
>> -0.097  -0.071  -0.993   2.262;
>> -0.047   0.997  -0.067   5.775;
>>  0.000   0.000   0.000   1.000;
>> float2int = 0
>> ---
>> ERROR: could not find orig as either mgz or COR
>> --- 
>>
>> -
>>
>>
>>
>> ___
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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 Partners
>>   Compliance HelpLine at
>>   http://www.partners.org/complianceline . If the e-mail was sent
>>   to you in error
>>   but does not contain patient information, please contact the
>>   sender and properly
>>   dispose of the e-mail.
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[Freesurfer] putamen seg

[Gregory Kirk]

Hi,

tried to use control points to improve the segmentation of the putamen in the
difficult area between putamen,claustrum & insula. adding some white matter 
control points does not seem to insluence the aseg segmentation. control points 
are set to 110 after reprocessing 
with recon-all -autorecon2-cp -autorecon3 -subjid 008 ( v5.1), but these same 
points are still labeled as putamen?

also i do see that some white matter filaments have leaked into the putamen, so 
the mailing list
comments that control points would mess it up seems it would be correct ( if it 
was affecting
the putamen seg, which it does not seem to have done at all).

so options are manual editing, here ask opinions, the extra tissue added 
between the putamen&insula it is doing consistently, so taking the unedited 
volumes, after checking there are no odd other things added or missing
might be more unbiased estimate, that volumes after several human raters had 
selectively removed a few voxels here and there ?

any opinions ?

thanks

greg
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Re: [Freesurfer] mri_cc segfault

[Nick Schmansky]

PPJ,

Hi, if you want, you can send me the input files (the two aseg's and the
lta) and i can try to replicate the segfault in a debugger.

also, if you want, there is a beta of the upcoming v5.2 which is posted
here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
which you could try.  hopefully that mri_cc doesnt segfault.

Nick



On Tue, 2012-12-18 at 12:46 -0200, Pedro Paulo de Magalhães Oliveira
Junior wrote:
> I'm having a segfault with mri_cc it's happening sometimes using
> FreeSurfer 5.1
> 
> 
> Searching the mailing list I saw a similar problem in 2008 but with no
> answers.
> 
> 
> The relevant portion of recon-all.log:
> 
> 
>  mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz
> -lta 
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta
>  c70eb728-c505-46c2-a2a1-1ed409c36ea1 
> 
> 
> will read input aseg from aseg.auto_noCCseg.mgz
> writing aseg with cc labels to aseg.auto.mgz
> will write lta
> as 
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta
> reading aseg
> from 
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/aseg.auto_noCCseg.mgz
> reading norm
> from 
> /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/norm.mgz
> 2358 voxels in left wm, 13846 in right wm, xrange [122, 136]
> searching rotation angles z=[-10  4], y=[-31 -17]
> ^Msearching scale 1 Z rot -9.8  ^Msearching scale 1 Z rot -9.5
>  ^Msearching scale 1 Z rot -9.3  ^Msearching scale 1 Z rot -9.0
>  ^Msearching scale 1 Z rot -8.8  ^Msearching scale 1 Z rot -8.5
>  ^Msearching scale 1 Z rot -8.3  ^Msearching scale 1 Z rot -8.0
>  ^Msearching scale 1 Z rot -7.8  ^Msearching scale 1 Z rot -7.5
>  ^Msearching scale 1 Z rot -7.3  ^Msearching scale 1 Z rot -7.0
>  ^Msearching scale 1 Z rot -6.8  ^Msearching scale 1 Z rot -6.5
>  ^Msearching scale 1 Z rot -6.3  ^Msearching scale 1 Z rot -6.0
>  ^Msearching scale 1 Z rot -5.8  ^Msearching scale 1 Z rot -5.5
>  ^Msearching scale 1 Z rot -5.3  ^Msearching scale 1 Z rot -5.0
>  ^Msearching scale 1 Z rot -4.8  ^Msearching scale 1 Z rot -4.5
>  ^Msearching scale 1 Z rot -4.3  ^Msearching scale 1 Z rot -4.0
>  ^Msearching scale 1 Z rot -3.8  ^Msearching scale 1 Z rot -3.5
>  ^Msearching scale 1 Z rot -3.3  ^Msearching scale 1 Z rot -3.0
>  ^Msearching scale 1 Z rot -2.8  ^Msearching scale 1 Z rot -2.5
>  ^Msearching scale 1 Z rot -2.3  ^Msearching scale 1 Z rot -2.0
>  ^Msearching scale 1 Z rot -1.8  
> ^Msearching scale 1 Z rot -1.5  ^Msearching scale 1 Z rot -1.3
>  ^Msearching scale 1 Z rot -1.0  ^Msearching scale 1 Z rot -0.8
>  ^Msearching scale 1 Z rot -0.5  ^Msearching scale 1 Z rot -0.3
>  ^Msearching scale 1 Z rot -0.0  ^Msearching scale 1 Z rot 0.2
>  ^Msearching scale 1 Z rot 0.5  ^Msearching scale 1 Z rot 0.7
>  ^Msearching scale 1 Z rot 1.0  ^Msearching scale 1 Z rot 1.2
>  ^Msearching scale 1 Z rot 1.5  ^Msearching scale 1 Z rot 1.7
>  ^Msearching scale 1 Z rot 2.0  ^Msearching scale 1 Z rot 2.2
>  ^Msearching scale 1 Z rot 2.5  ^Msearching scale 1 Z rot 2.7
>  ^Msearching scale 1 Z rot 3.0  ^Msearching scale 1 Z rot 3.2
>  ^Msearching scale 1 Z rot 3.5  ^Msearching scale 1 Z rot 3.7  global
> minimum found at slice 129.0, rotations (-2.52, -3.27)
> final transformation (x=129.0, yr=-2.521, zr=-3.273):
>  0.997   0.057  -0.044  -2.975;
> -0.057   0.998   0.003  -6.742;
>  0.044  -0.000   0.999  -9.547;
>  0.000   0.000   0.000   1.000;
> Segmentation fault
> 
> 
> Thanks
> 
> 
> PPJ
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
> 
> 
> 
> 
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Re: [Freesurfer] Error in using tkregister2

[Douglas N Greve]

Is $SUBJECTS_DIR/$subject exist?


On 12/18/2012 05:13 PM, priyank wrote:
> I have these files in the folder 18135.
> 18135.RS.mgz   18135_RS_register.dat.log 
> 18135_RS_register.dat.sum
> 18135.RS+orig.BRIK 18135_RS_register.dat.log.old 
> 18135.RS.template.mgz
> 18135.RS+orig.HEAD 18135_RS_register.dat.mincost
> 18135_RS_register.dat  18135_RS_register.dat.param
>
> and other freesurfer files in the folder 18135_FS (in the respective 
> folders.. mri, surf...)...
>
> I copied 18135.RS.mgz in the 18135_FS/mri/orig folder also.
>
> I have tried both directories to be SUBJECTS_DIR but it didn't work.
>
> Do I need to move all the files in 18135_FS/mri/orig folder?
>
>
> On 12/18/2012 4:38 PM, Bruce Fischl wrote:
>> what is your SUBJECTS_DIR env variable?
>> On Tue, 18 Dec 2012, priyank wrote:
>>
>>> Hi,
>>>   I am using the command to check my registration and getting this
>>> error message: could not find orig as either mgz or COR. This is the
>>> command I am using.
>>>   tkregister2 --mov 18135.RS.mgz --reg 18135_RS_register.dat --surf
>>> OUTPUT--
>>>  
>>>
>>> INFO: no target volume specified, assuming FreeSurfer orig volume.
>>> target  volume orig
>>> movable volume 18135.RS.mgz
>>> reg file   18135_RS_register.dat
>>> LoadVol1
>>> ZeroCRAS   0
>>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
>>> Diagnostic Level -1
>>>  Input registration matrix 
>>> -0.994  -0.040   0.100   2.799;
>>> -0.097  -0.071  -0.993   2.262;
>>> -0.047   0.997  -0.067   5.775;
>>>  0.000   0.000   0.000   1.000;
>>> float2int = 0
>>> ---
>>> ERROR: could not find orig as either mgz or COR
>>> 
>>>  
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>
>>
>> The information in this e-mail is intended only for the person to 
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and 
>> the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to 
>> you in error
>> but does not contain patient information, please contact the sender 
>> and properly
>> dispose of the e-mail.
>>
>
>
>
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Re: [Freesurfer] L-R Volume Flipping

[Douglas Greve]

Hi Donald, it might be the case. If the fmri has an ordering such that 
the columns increase as you go from left to right, then they will have 
to be reversed when you map them to the orig.mgz. This is generally not 
a problem because we always keep track of which side is left and right. 
If you are using a visualization tool that does not read in and act on 
the geometry, then things can appear to flip around.


doug


On 12/18/12 8:47 PM, MCLAREN, Donald wrote:

Dear All,

I've noticed something strange with some data I'm helping to process:

When looking at the L/R asymmetry in the brains (attached), the images
seem to flip after bbregister/mri_vol2vol. The exact commands:
bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2
mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg
register.dat --no-resample --o transformed_fMRI.nii

I've attached a document that shows the flipping. You'll notice the
highest point of the ventricle flips sides after
bbregister/mri_vol2vol. Any thoughts on what is going on would be
appreciated.

The contents of register.dat are as follows:
FS_D011
3.00
3.54
0.15
-9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02
1.619825601577759e+00
6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01
-1.230294322967529e+01
4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01
-1.072110843658447e+01
0 0 0 1
round


Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


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Re: [Freesurfer] volume of interest

[Douglas Greve]

That code looks correct. It should match the scanner coordinates. Does 
the volume geometry (ie, vox2ras) in the labelMRI.mgz file match that of 
the orig.mgz/T1.mgz?


doug

On 12/18/12 6:10 PM, octavian lie wrote:


Dear Douglas,

I adapted the following script to get the RAS coordinates:
segmri = MRIread(labelMRI.mgz); %labelMRI is the input resection 
volume .mgz

segid =1;
% Get list of voxels with seg id
indlab = find(segmri.vol == segid);
nlab = length(indlab);

% Convert indices to row, col, slice
[r c s] = ind2sub(segmri.volsize,indlab);
crs = [c r s]' - 1 ; % 0-based
crs = [crs; ones(1,nlab)];

% Convert row, col, slice to XYZ
xyz1 = segmri.vox2ras0 * crs;
xyz = xyz1(1:3,:)';
inspecting the xyz matrix, copying individual RAS coordinates from xyz 
to tkmedit volume RAS field, and noting the RAS coordinates of the 
boundaries in the R,A,S, directions, it looks like x and y/ R and A 
are ok, but the S/z is off, closer in nos with the volume scanner 
coordinates. I could not figure out why this is. I mention that the 
labelMRI.mgz  was generated by using mri_convert on a labelMRI.nii 
mask file imported from itksnap without additional flags.
Please advise, I also mention that the labelMRI.mgz file aligns well 
in tkmedit with the patient's T1.mgz.

Below I paste the mri_info on labelMRI.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1., 1., 1.
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -1., y_r = -0., z_r = -0., c_r = -0.2196
: x_a = -0., y_a = 0., z_a = 1., c_a = 1.9029
: x_s = 0., y_s = -1., z_s = 0., c_s = 28.2156

talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal

voxel to ras transform:
-1. -0. -0. 127.7804
-0. 0. 1. -126.0971
0. -1. 0. 156.2156
0. 0. 0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
-1. 0. 0. 127.7804
-0. -0. -1. 156.2156
-0. 1. -0. 126.0971
0. 0. 0. 1.
Thank you very much,
Octavian.


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] L-R Volume Flipping

[MCLAREN, Donald]

Thanks, that's what I thought might be happening. I'll check a few
different programs to see if I can recover the correct orientation. If
we need to reverse the images, would you recommend doing it before or
after the bbregister step? Would it be sufficient just to change the
header of the image or do we need to physically change the data?

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve
 wrote:
> Hi Donald, it might be the case. If the fmri has an ordering such that the
> columns increase as you go from left to right, then they will have to be
> reversed when you map them to the orig.mgz. This is generally not a problem
> because we always keep track of which side is left and right. If you are
> using a visualization tool that does not read in and act on the geometry,
> then things can appear to flip around.
>
> doug
>
>
>
> On 12/18/12 8:47 PM, MCLAREN, Donald wrote:
>
> Dear All,
>
> I've noticed something strange with some data I'm helping to process:
>
> When looking at the L/R asymmetry in the brains (attached), the images
> seem to flip after bbregister/mri_vol2vol. The exact commands:
> bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2
> mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg
> register.dat --no-resample --o transformed_fMRI.nii
>
> I've attached a document that shows the flipping. You'll notice the
> highest point of the ventricle flips sides after
> bbregister/mri_vol2vol. Any thoughts on what is going on would be
> appreciated.
>
> The contents of register.dat are as follows:
> FS_D011
> 3.00
> 3.54
> 0.15
> -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02
> 1.619825601577759e+00
> 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01
> -1.230294322967529e+01
> 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01
> -1.072110843658447e+01
> 0 0 0 1
> round
>
>
> Best Regards, Donald McLaren
> =
> D.G. McLaren, Ph.D.
> Research Fellow, Department of Neurology, Massachusetts General Hospital and
> Harvard Medical School
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Website: http://www.martinos.org/~mclaren
> Office: (773) 406-2464
> =
> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
> intended only for the use of the individual or entity named above. If the
> reader of the e-mail is not the intended recipient or the employee or agent
> responsible for delivering it to the intended recipient, you are hereby
> notified that you are in possession of confidential and privileged
> information. Any unauthorized use, disclosure, copying or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited and may be unlawful. If you have received this e-mail
> unintentionally, please immediately notify the sender via telephone at (773)
> 406-2464 or email.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Re: [Freesurfer] L-R Volume Flipping

[Douglas Greve]

I would not just reverse the images. If something is going wrong with 
bbregister/mri_vol2vol then it should be fixed. If you don't keep 
careful track of these things and know exactly what is happening, then 
it will certainly come back to bite you (or me!).
doug





On 12/18/12 11:26 PM, MCLAREN, Donald wrote:
> Thanks, that's what I thought might be happening. I'll check a few
> different programs to see if I can recover the correct orientation. If
> we need to reverse the images, would you recommend doing it before or
> after the bbregister step? Would it be sufficient just to change the
> header of the image or do we need to physically change the data?
>
> Best Regards, Donald McLaren
> =
> D.G. McLaren, Ph.D.
> Research Fellow, Department of Neurology, Massachusetts General Hospital and
> Harvard Medical School
> Postdoctoral Research Fellow, GRECC, Bedford VA
> Website: http://www.martinos.org/~mclaren
> Office: (773) 406-2464
> =
> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
> intended only for the use of the individual or entity named above. If the
> reader of the e-mail is not the intended recipient or the employee or agent
> responsible for delivering it to the intended recipient, you are hereby
> notified that you are in possession of confidential and privileged
> information. Any unauthorized use, disclosure, copying or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited and may be unlawful. If you have received this e-mail
> unintentionally, please immediately notify the sender via telephone at (773)
> 406-2464 or email.
>
>
> On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve
>  wrote:
>> Hi Donald, it might be the case. If the fmri has an ordering such that the
>> columns increase as you go from left to right, then they will have to be
>> reversed when you map them to the orig.mgz. This is generally not a problem
>> because we always keep track of which side is left and right. If you are
>> using a visualization tool that does not read in and act on the geometry,
>> then things can appear to flip around.
>>
>> doug
>>
>>
>>
>> On 12/18/12 8:47 PM, MCLAREN, Donald wrote:
>>
>> Dear All,
>>
>> I've noticed something strange with some data I'm helping to process:
>>
>> When looking at the L/R asymmetry in the brains (attached), the images
>> seem to flip after bbregister/mri_vol2vol. The exact commands:
>> bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2
>> mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg
>> register.dat --no-resample --o transformed_fMRI.nii
>>
>> I've attached a document that shows the flipping. You'll notice the
>> highest point of the ventricle flips sides after
>> bbregister/mri_vol2vol. Any thoughts on what is going on would be
>> appreciated.
>>
>> The contents of register.dat are as follows:
>> FS_D011
>> 3.00
>> 3.54
>> 0.15
>> -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02
>> 1.619825601577759e+00
>> 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01
>> -1.230294322967529e+01
>> 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01
>> -1.072110843658447e+01
>> 0 0 0 1
>> round
>>
>>
>> Best Regards, Donald McLaren
>> =
>> D.G. McLaren, Ph.D.
>> Research Fellow, Department of Neurology, Massachusetts General Hospital and
>> Harvard Medical School
>> Postdoctoral Research Fellow, GRECC, Bedford VA
>> Website: http://www.martinos.org/~mclaren
>> Office: (773) 406-2464
>> =
>> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
>> intended only for the use of the individual or entity named above. If the
>> reader of the e-mail is not the intended recipient or the employee or agent
>> responsible for delivering it to the intended recipient, you are hereby
>> notified that you are in possession of confidential and privileged
>> information. Any unauthorized use, disclosure, copying or the taking of any
>> action in reliance on the contents of this information is strictly
>> prohibited and may be unlawful. If you have received this e-mail
>> unintentionally, please immediately notify the sender via telephone at (773)
>> 406-2464 or email.
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the
>>

Re: [Freesurfer] volume of interest

[Douglas Greve]

There are several "RAS" coordinates in tkmedit. One is scanner coords 
(vol2ras), the other is "volume RAS" coordinates (tkrvox2ras).

doug



On 12/18/12 11:31 PM, octavian lie wrote:

Dear Douglas,
yes, it matches the T1. I am interested though in matching the volume 
RAS as it appears in tkmedit, so I changed the code to use tkrvox2ras 
instead of vox2ras0.

Thank you,
octavian.

On Tue, Dec 18, 2012 at 10:23 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



That code looks correct. It should match the scanner coordinates.
Does the volume geometry (ie, vox2ras) in the labelMRI.mgz file
match that of the orig.mgz/T1.mgz?

doug


On 12/18/12 6:10 PM, octavian lie wrote:


Dear Douglas,

I adapted the following script to get the RAS coordinates:
segmri = MRIread(labelMRI.mgz); %labelMRI is the input resection
volume .mgz
segid =1;
% Get list of voxels with seg id
indlab = find(segmri.vol == segid);
nlab = length(indlab);

% Convert indices to row, col, slice
[r c s] = ind2sub(segmri.volsize,indlab);
crs = [c r s]' - 1 ; % 0-based
crs = [crs; ones(1,nlab)];

% Convert row, col, slice to XYZ
xyz1 = segmri.vox2ras0 * crs;
xyz = xyz1(1:3,:)';
inspecting the xyz matrix, copying individual RAS coordinates
from xyz to tkmedit volume RAS field, and noting the RAS
coordinates of the boundaries in the R,A,S, directions, it looks
like x and y/ R and A are ok, but the S/z is off, closer in nos
with the volume scanner coordinates. I could not figure out why
this is. I mention that the labelMRI.mgz  was generated by using
mri_convert on a labelMRI.nii mask file imported from itksnap
without additional flags.
Please advise, I also mention that the labelMRI.mgz file aligns
well in tkmedit with the patient's T1.mgz.
Below I paste the mri_info on labelMRI.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1., 1., 1.
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -1., y_r = -0., z_r = -0., c_r =
-0.2196
: x_a = -0., y_a = 0., z_a = 1., c_a = 1.9029
: x_s = 0., y_s = -1., z_s = 0., c_s = 28.2156

talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal

voxel to ras transform:
-1. -0. -0. 127.7804
-0. 0. 1. -126.0971
0. -1. 0. 156.2156
0. 0. 0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
-1. 0. 0. 127.7804
-0. -0. -1. 156.2156
-0. 1. -0. 126.0971
0. 0. 0. 1.
Thank you very much,
Octavian.


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.




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