date:20140428

Thank you very much!
A last question, please. Therefore, do you are working also on SLF I and SLF II 
implementation in TRACULA? If yes, how much time might be required to do it? 
(I'm writing a paper and I may wait these new tracts).

Stefano

Messaggio originale
Da: fis...@nmr.mgh.harvard.edu
Data: 28-apr-2014 1.54
A: , "Freesurfer support 
list"
Ogg: Re: [Freesurfer] ROI in FreeSurferColorLUT.txt

Hi Stefano

sorry, those are not ready yet, and the tracts do come from tracula
Bruce
On Mon, 
28 Apr 2014, std...@virgilio.it wrote:

> Hi list, 
> I'm noting these regions in FreeSurferColorLUT.txt. How can I obtained
> structural information from them?
>
>  8001  Thalamus-Anterior 74  130 181 0
>  8002  Thalamus-Ventral-anterior 242 241 240 0
>  8003  Thalamus-Lateral-dorsal   206 65  78  0
>  8004  Thalamus-Lateral-posterior120 21  133 0
>  8005  Thalamus-Ventral-lateral  195 61  246 0
>  8006  Thalamus-Ventral-posterior-medial 3   147 6   0
>  8007  Thalamus-Ventral-posterior-lateral220 251 163 0
>  8008  Thalamus-intralaminar 232 146 33  0
>  8009  Thalamus-centromedian 4   114 14  0
>  8010  Thalamus-mediodorsal  121 184 220 0
>  8011  Thalamus-medial   235 11  175 0
>  8012  Thalamus-pulvinar 12  46  250 0
>  8013  Thalamus-lateral-geniculate   203 182 143 0
>  8014  Thalamus-medial-geniculate42  204 167 0
> 
> and from 
> 
> 6010   Left-SLF1236 16  231 0
> 
> 6020   Right-SLF1   237 18  232 0
> 
> 6030   Left-SLF3236 13  227 0
> 6040   Right-SLF3   236 17  228 0
> 
> 6050   Left-CST 1   255 1   0
> 6060   Right-CST2   255 1   0
> 
> 6070   Left-SLF2236 14  230 0
> 6080   Right-SLF2   237 14  230 0
> 
> Are the tracts different from tracts product by TRACULA? and can I use them 
> with TRACULA outputs?
> 
> Thanks, 
> 
> Stefano
> 
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Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3

I think there is - look in the view menu. There is also something in 
freeview that Ruopeng can point you at.

cheers
Bruce
On Sun, 27 Apr 2014, prasser wrote:

> Thanks for your reply.
> 
> Yes, I can upload the data. Is there a private area I can upload to?
> 
> Also, is there a flag that enables acquisition slice space info to be used
> with tkmedit?
> 
> Lastly, when converting to .nii with other packages and viewing with tkmedit
> the acquisition slice space seems to be taken into account.
> 
> Paul
> 
> 
> 
> 
> 
>  On Sun, 27 Apr 2014 17:33:02 -0700 Bruce Fischl
>  wrote 
>
>   Hi Paul
>
>   perhaps Ruopeng can comment, but I suspect this isn't a problem
>   - it's
>   just showing it to you in a standard anatomical space not the
>   slice spaceit
>   was acquired in. If you want to upload the dataset we can take a
>   look and
>   confirm
>
>   cheers
>   Bruce
> 
>
>   On Sun, 27 Apr 2014, prasser wrote:
>
>   > Hi,
>   >
>   > I am still having some concerns using mri_convert on Skyra
>   volumes that I'm
>   > hoping can please be addressed.
>   >
>   > On this occasion I have used mri_convert to convert a single
>   dicom file to
>   > nifti from a volume collected on a siemens Skyra scanner using
>   Freesurfer5.3
>   > on CentOS5.7.
>   >
>   > When viewing this nifti image using tkmedit it appears
>   'cut-up' over many
>   > sagittal slices (please see attached) rather than the whole
>   image appearing
>   > on one plane.
>   >
>   > Not sure if this is an issue with tkmedit or mri_convert?
>   >
>   > This problem persists if i convert the entire volume, with
>   this 'cutting'
>   > appearing as vertical lines in the image.
>   >
>   > This is also the case when using the new mri_convert patch for
>   OS X.
>   >
>   > Lastly, I can upload a dicom file if needed.
>   >
>   > Thanks,
>   > Paul
>   >
>   >
>   >
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Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

2014-04-28 Thread Alan Francis

Thanks Eugenio.


On Mon, Apr 28, 2014 at 3:18 AM, Eugenio Iglesias wrote:

> Dear all,
> the current module in FreeSurfer works with 1mm T1 data, by relying on
> strong shape priors. So, at this point, feeding the algorithm data from a
> 3T scanner or a 1.5T scanner is pretty much the same.
> Joshua, it is indeed inaccurate to say that the method relies on a
> generated hippocampal surface, but you are definitely right regarding the
> SLRM: it is not modeled at this point (we have a new version that models it
> coming out hopefully soon!).
> Cheers,
> /Eugenio
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> - Original Message -
> From: "Joshua Lee" 
> To: "Freesurfer support list" 
> Sent: Friday, April 25, 2014 2:10:29 AM
> Subject: Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla
>
>
>
>
> Hi Alan,
>
> Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x
> 0.4 mm in-plane resolution). The thickness of a CA subfield typically range
> between 0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter
> resolutions. Further, subfield segmentation typically requires
> high-contrast data to discern the internal boundaries formed by the stratum
> radiatum/stratum lacunosum-moleculare (SLRM). I doubt that images produced
> on a 1.5 T magnet can achieve the necessary contrast. Last, and please
> someone correct me if what I say is inaccurate, but doesn't the Van Leemput
> method use statistical priors to apply label probabilities in reference to
> a generated hippocampal surface? This would imply that the method assigns
> label probabilities without reference to a subject's SLRM intensity
> information. For volumetry, I am somewhat skeptical that a method that only
> relies on a generated surface would be sensitive to group x subfield
> interactions; especially double dissociations in which overall volume/shape
> of the hippocampus may be similar across groups. That the that was
> generated from potentially low resolution, low contrast data cannot help
> the matter. Some may disagree about this though and I'd be interested in
> hearing what other people think about the matter. In general, I am quite
> optimistic about automated methods to segment the subfields.
>
>
>
>
> Joshua
>
>
>
>
>
>
>
> -
>
> Joshua K. Lee
> Doctoral Candidate
>
> Department of Psychology &
> Center for Mind and Brain University of California, Davis
>
>
>
>
> On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis < alandarkene...@gmail.com> 
> wrote:
>
>
>
> Hi Bruce and FreeSurfers:
>
> I have received a manuscript to review for possible publication. The
> authors have used the subfields algorithm on 1.5T scans and obtained a
> parcellation with values. They have drawn some major conclusions on the
> basis of the findings. My understanding is that this method can only be
> done on 3T. Is the 1.5T results valid?
>
> Please advice.
>
> thanks,
>
> Alan Francis
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Re: [Freesurfer] longitudinal recon-all -long error

2014-04-28 Thread Martin Reuter


Hi Corinna,

try to open
/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz

in freeview to see if maybe the file is corrupted.

Best, Martin


On 04/25/2014 03:46 PM, Corinna Bauer wrote:

Hello,
I am on the recon-all -long step of the longitudinal processing stream 
and the final time point exits with errors at the mri_convert stage.


mri_convert -at 
/home/Documents/longitudinal_morph/meta/test_subject_template/mri/transforms/test_subject_2ndpostop_to_test_subject_template.lta 
-odt uchar -rt cubic 
/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz 
/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop.long.test_subject_template/mri/orig.mgz 



mghRead(/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz): 
could not read 262144 bytes at slice 4


I still have plenty of space left on the drive


 total   used   free shared buffers cached
Mem:  16348132   148565241491608  0 5349166193928
-/+ buffers/cache:81276808220452
Swap: 16690172 573232   16116940



Any suggestions? The two previous timepoints finished without error.


Corinna


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Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
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Re: [Freesurfer] longitudinal recon-all -long error

2014-04-28 Thread Corinna Bauer

Hi Martin,
Neither freeview nor tkmedit could open the 001.mgz file. It could not read
262144 bytes at slice 4. At this point is my best option to re-run this
time point from the beginning?

Corinna



On Mon, Apr 28, 2014 at 9:18 AM, Martin Reuter
wrote:

>  Hi Corinna,
>
> try to open
>
> /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz
>
> in freeview to see if maybe the file is corrupted.
>
> Best, Martin
>
>
>
> On 04/25/2014 03:46 PM, Corinna Bauer wrote:
>
>  Hello,
> I am on the recon-all -long step of the longitudinal processing stream and
> the final time point exits with errors at the mri_convert stage.
>
> mri_convert -at
> /home/Documents/longitudinal_morph/meta/test_subject_template/mri/transforms/test_subject_2ndpostop_to_test_subject_template.lta
> -odt uchar -rt cubic
> /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz
> /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop.long.test_subject_template/mri/orig.mgz
>
>
> mghRead(/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz):
> could not read 262144 bytes at slice 4
>
>  I still have plenty of space left on the drive
>
>
>  total   used   free sharedbuffers cached
> Mem:  16348132   148565241491608  0 5349166193928
> -/+ buffers/cache:81276808220452
> Swap: 16690172 573232   16116940
>
>
>
>  Any suggestions? The two previous timepoints finished without error.
>
>
> Corinna
>
>
> ___
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> Martin Reuter, Ph.D.
>
> Instructor in Neurology
>   Harvard Medical School
> Assistant in Neuroscience
>   Dept. of Radiology, Massachusetts General Hospital
>   Dept. of Neurology, Massachusetts General Hospital
> Research Affiliate
>   Computer Science and Artificial Intelligence Lab,
>   Dept. of Electrical Engineering and Computer Science,
>   Massachusetts Institute of Technology
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> Web  : http://reuter.mit.edu
>
>
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Re: [Freesurfer] normalization problem (versions 5.1 and 5.3)


Hi Maia

it's hard to know from just these images, but I wonder whether the high 
background noise level at the top of the image is messing up 5.1. You 
might try cropping that out and seeing if things get better.


cheers
Bruce
On Fri, 25 Apr 
2014, Maia Pujara wrote:



Hi all,
After running 200+ subjects through recon-all using version 5.1, all but 30
came back with complete surfaces. The 30 that failed seem to have the same
problem with normalization. 

After re-running these 30 subjects with v5.3, we were able to get a good
quality brainmask.mgz output, which was not the case when we ran these
subjects through v5.1. See attached for comparisons of v5.1 and v5.3
outputs.

Would we need to be adding additional flags to get 5.1 to produce usable
results for these subjects? Or might there be some other workaround for
this? 

Thanks in advance!
Maia

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Re: [Freesurfer] Catastrophic Surface Inaccuracies

2014-04-28 Thread Jonathan Holt

Bruce,

I dont see any WM connections that jump out at me. Could I upload it and have a 
second opinion?

Jon
On Apr 25, 2014, at 11:33 PM, Bruce Fischl  wrote:

> Hi Jon
> 
> in this kind of case the default method did the wrong thing (closing the hole 
> instead of cutting the handle). You need to identify the incorrectly 
> segmented voxels that cause the spurious correction and delete them from the 
> wm.mgz, then run autorecon2-wm autorecon3
> 
> cheers
> Bruce
> 
> 
> On Fri, 25 Apr 2014, Jonathan Holt wrote:
> 
>> Thanks Bruce,
>> 
>> I’ll check for such wm connections. Is this the default method for 
>> correcting topology issues?
>> 
>> jon
>> On Apr 25, 2014, at 10:59 PM, Bruce Fischl  
>> wrote:
>> 
>>> Hi Jon
>>> 
>>> that is almost certainly a topology correction problem. Check to see if the 
>>> wm.mgz contains any spurious connections that cause the space that is 
>>> missing in the ?h.white surface to be closed in a slice. If you upload the 
>>> data we can show you how to correct it if you want.
>>> 
>>> cheers
>>> Bruce
>>> On Fri, 25 Apr 2014, Jonathan Holt wrote:
>>> 
 Hi all,
 I would love information on how best to tackle and alleviate this type of 
 surface issue. Images
 attached.
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Re: [Freesurfer] longitudinal recon-all -long error

2014-04-28 Thread Martin Reuter

Hi Corinna,

the 001.mgz is the first file created in the cross sectional stream
(when you import your dicom) it is the input image to the stream and
just the dicom converted into mgz format. If it is corrupted, you should
rerun this cross sectional time point (just to be safe), the base and
the all the long runs.

Best, Martin

On 04/28/2014 09:31 AM, Corinna Bauer wrote:

Hi Martin,
Neither freeview nor tkmedit could open the 001.mgz file. It could not
read 262144 bytes at slice 4. At this point is my best option to
re-run this time point from the beginning?

Corinna

On Mon, Apr 28, 2014 at 9:18 AM, Martin Reuter
mailto:mreu...@nmr.mgh.harvard.edu>> wrote:

Hi Corinna,

try to open

/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz

in freeview to see if maybe the file is corrupted.

Best, Martin

On 04/25/2014 03:46 PM, Corinna Bauer wrote:

Hello,
I am on the recon-all -long step of the longitudinal processing
stream and the final time point exits with errors at the
mri_convert stage.

mri_convert -at

/home/Documents/longitudinal_morph/meta/test_subject_template/mri/transforms/test_subject_2ndpostop_to_test_subject_template.lta
-odt uchar -rt cubic

/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz

/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop.long.test_subject_template/mri/orig.mgz

mghRead(/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz):
could not read 262144 bytes at slice 4

I still have plenty of space left on the drive

total used free sharedbuffers cached
Mem: 16348132 14856524 1491608 0 534916
6193928

-/+ buffers/cache:81276808220452
Swap: 16690172 573232 16116940

Any suggestions? The two previous timepoints finished without error.

Corinna

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Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone:+1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web :http://reuter.mit.edu

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149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

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reu...@mit.edu
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Re: [Freesurfer] Catastrophic Surface Inaccuracies


sure
On Mon, 28 Apr 2014, Jonathan Holt wrote:


Bruce,

I dont see any WM connections that jump out at me. Could I upload it and have a 
second opinion?

Jon
On Apr 25, 2014, at 11:33 PM, Bruce Fischl  wrote:


Hi Jon

in this kind of case the default method did the wrong thing (closing the hole 
instead of cutting the handle). You need to identify the incorrectly segmented 
voxels that cause the spurious correction and delete them from the wm.mgz, then 
run autorecon2-wm autorecon3

cheers
Bruce


On Fri, 25 Apr 2014, Jonathan Holt wrote:


Thanks Bruce,

I’ll check for such wm connections. Is this the default method for correcting 
topology issues?

jon
On Apr 25, 2014, at 10:59 PM, Bruce Fischl  wrote:


Hi Jon

that is almost certainly a topology correction problem. Check to see if the 
wm.mgz contains any spurious connections that cause the space that is missing 
in the ?h.white surface to be closed in a slice. If you upload the data we can 
show you how to correct it if you want.

cheers
Bruce
On Fri, 25 Apr 2014, Jonathan Holt wrote:


Hi all,
I would love information on how best to tackle and alleviate this type of 
surface issue. Images
attached.

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Re: [Freesurfer] Problem with Monte Carlo Simulation


No, I mean using the --cache option which will use precomputed tables 
rather than generating new ones

On 04/24/2014 08:01 PM, Jacqueline Elaine Fitzgerald wrote:
> Hi Doug,
>
> Thank you for your reply. By precomputed do you mean the FDR in the 
> GUI? Apologies I'm still new to the program!
>
> I am planning on running an ROI analysis so will need to run it for 
> that anyway (I think?)
>
> Best,
>
> Jackie
>
>
> On 24 April 2014 21:47, Douglas N Greve  > wrote:
>
>
> First of all, do you really need to run the simulation? If you are
> just
> doing a whole hemisphere analysis on fsaverage, then you can use the
> precomputed option.
>
> doug
>
> On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote:
> > Hi,
> >
> > I am having problem when running the Monte Carlo script. The script
> > seems to fail after only a few simulations but it does not give
> me any
> > error message, it just says 'killed'. I am running it on 126
> > participants (2 groups of 63) and I have tried it on a number of
> > different measures (sulc, area etc.). I thought it may be an space
> > issue but I cleared all other files but that did not seem to
> make any
> > difference.
> >
> > This is what is printed out on the terminal:
> >
> > [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15
> > --sim mc-z 1 1.3 mc-z.negative --sim-sign neg --overwrite
> >
> > cmdline mri_glmfit --y
> > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd
> >
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods
> > --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15
> > --surf fsaverage rh --label
> >
> /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C
> >
> 
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat
> > --C
> >
> 
> /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat
> >
> >
> >
> > WARNING: unrecognized mri_glmfit cmd option dods
> >
> >
> > SURFACE: fsaverage rh
> >
> > /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim
> >
> > --glmdir Rh_JacobianW_15 --sim mc-z 1 1.3 mc-z.negative
> --sim-sign
> > neg --overwrite
> >
> > $Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $
> >
> > Thu Apr 24 18:58:31 IST 2014
> >
> > Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed
> Oct 16
> > 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux
> >
> > fitzgeje
> >
> > setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/
> >
> > FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0
> >
> > DoPoll = 0
> >
> > DoPBSubmit = 0
> >
> > DoBackground = 0
> >
> > DiagCluster = 0
> >
> > gd2mtx = dods
> >
> > fwhm = 21.770250
> >
> > nSimPerJob = 1
> >
> > 1/1 Thu Apr 24 18:58:31 IST 2014
> >
> > mri_glmfit --y
> > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C
> >
> 
> Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx
> > --C
> >
> 
> Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx
> > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 1 1.3
> > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm
> 21.770250
> > --fsgd Rh_JacobianW_15/y.fsgd dods --label
> > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label
> > --surf fsaverage rh white
> >
> > INFO: ignoring tag Creator
> >
> > INFO: ignoring tag SUBJECTS_DIR
> >
> > INFO: ignoring tag SynthSeed
> >
> > reading group avg surface area 822 cm^2 from file
> >
> > Reading in average area
> >
> /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
> >
> > reading group avg surface area 822 cm^2 from file
> >
> > Reading in average area
> >
> /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh
> >
> > simbase Rh_JacobianW_15/csd/mc-z.negative.j001
> >
> > gdfReadHeader: reading Rh_JacobianW_15/y.fsgd
> >
> > INFO: demeaning continous variables
> >
> > Continuous Variable Means (all subjects)
> >
> > Class Means of each Continuous Variable
> >
> > 1 groupASD
> >
> > 2 groupCTRL
> >
> > INFO: gd2mtx_method is dods
> >
> > Reading source surface
> > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white
> >
> > Number of vertices 163842
> >
> > Number of faces327680
> >
> > Total area 65020.765625
> >
> > AvgVtxArea   0.396850
>

Re: [Freesurfer] labels of thalami

Use mri_cor2label

On 04/28/2014 01:11 PM, std...@virgilio.it wrote:
> Hi list,
>
> I'd like to obtained .labels of thalami to use it in FSL.
>
> How can I do it?
>
> Thanks,
>
>
> Stefano
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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[Freesurfer] R: labels of thalami

My apology. Here, the responce
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32645.html


Messaggio originale

Da: std...@virgilio.it

Data: 28-apr-2014 19.11

A: 

Ogg: [Freesurfer] labels of thalami



Hi list, 
I'd like to obtained .labels of thalami to use it in FSL.
How can I do it?
Thanks,

Stefano   



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[Freesurfer] R: Re: labels of thalami

Thank you very much!!

Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 28-apr-2014 19.21
A: 
Ogg: Re: [Freesurfer] labels of thalami

Use mri_cor2label

On 04/28/2014 01:11 PM, std...@virgilio.it wrote:
> Hi list,
>
> I'd like to obtained .labels of thalami to use it in FSL.
>
> How can I do it?
>
> Thanks,
>
>
> Stefano
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] labels of thalami

Hi list, 
I'd like to obtained .labels of thalami to use it in FSL.
How can I do it?
Thanks,

Stefano   ___
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[Freesurfer] Extract ROI from anatomical volume

2014-04-28 Thread pfotiad

Hi FS experts,

I was wondering what the best way to extract an ROI from an anatomical
volume would be. For instance, I would like to create a volume of only the
wm-lh-precentral based on the orig.mgz volume and on the segmentation map
wmparc.mgz. I know that something similar can be done with the
mri_extract_label command, but if I'm not mistaken that command can only
be applied to a segmentation volume, and not on an anatomical volume like
orig.mgz.

Thanks in advance,
Panos
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Re: [Freesurfer] Segmentatoin fault using Freesurfer Functions Fedora 19 - Freesurfer 5.1

2014-04-28 Thread Nick Schmansky, MGH

John,

Have you tried the Centos6_x86_64 build of freesurfer on Fedora 19?  The
Centos4_x86_64 build is built against a rather old kernel, and likely to
go away soon anyway.

Generally a debug build is not of much use for tkmedit seg-faults.  If
you still have trouble after trying the centos6 build, and the segfaults
occur with mri_convert using data contained within freesurfer's sample
subjects dir (freesurfer/subjects), then we can send a debug build of
mri_convert.

Nick

On Sat, 2014-04-26 at 13:03 +, West, John D. wrote:
> Hi Bruce.
> 
> Thanks so much for the offer of help.  I would really appreciate it.
> If you can send me the files and then let me know what I need to
> capture I'll try it out.
> 
> Thanks.
> -John
> 
> Sent from my Windows Phone
> 
> __
> From:Bruce Fischl
> Sent:‎4/‎25/‎2014 11:38 PM
> To:Freesurfer support list
> Subject:Re: [Freesurfer] Segmentatoin fault using Freesurfer Functions
> Fedora 19 - Freesurfer 5.1
> 
> 
> Hi John
> 
> we could give you a version with debugging info and source and you
> could 
> run it in gdb and find out where it is crashing. Or you could send us
> the 
> core fie from a version with debugging on
> 
> cheers
> Bruce
> 
> On Fri, 25 Apr 2014, West, 
> John D. wrote:
> 
> > 
> > Hello.
> > 
> > 
> > We are trying to get Freesurfer 5.1 to work on Fedora 19.  The
> functions we have tried show the help
> > menu successfully when asked, but run into a Segmentation Fault when
> trying to process anything.  Both
> > tkmedit and mri_convert have shown this behavior.  Segmentation
> Faults are notoriously hard to track
> > down, but do you have any suggestions as to what may be causing
> this?  This version of freesurfer seems
> > to work fine on fedora 17 and older.
> > 
> >  
> > 
> > We are using the CentOS4 x86_64 version of Freesurfer 5.1.
> > 
> >  
> > 
> > Thanks.
> > 
> > -John West
> > 
> > Systems Administrator
> > 
> > IU Center for Neuroimaging
> > 
> > 
> >
> ___
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Re: [Freesurfer] Extract ROI from anatomical volume

Hi Panos

so you want an intensity volume that is zero everywhere except in a 
label? If so, try mri_mask

cheers
Bruce

On Mon, 28 Apr 2014, pfot...@nmr.mgh.harvard.edu wrote:

> Hi FS experts,
>
> I was wondering what the best way to extract an ROI from an anatomical
> volume would be. For instance, I would like to create a volume of only the
> wm-lh-precentral based on the orig.mgz volume and on the segmentation map
> wmparc.mgz. I know that something similar can be done with the
> mri_extract_label command, but if I'm not mistaken that command can only
> be applied to a segmentation volume, and not on an anatomical volume like
> orig.mgz.
>
> Thanks in advance,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] R: R: Re: labels of thalami

My apologies, but how can I visualize and check the labels obtained by 
mri_cor2label?
Thanks, 

Stefano

Messaggio originale

Da: std...@virgilio.it

Data: 28-apr-2014 19.23

A: 

Ogg: [Freesurfer] R: Re:  labels of thalami

Thank you very much!!

Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 28-apr-2014 19.21
A: 
Ogg: Re: [Freesurfer] labels of thalami

Use mri_cor2label

On 04/28/2014 01:11 PM, std...@virgilio.it wrote:
> Hi list,
>
> I'd like to obtained .labels of thalami to use it in FSL.
>
> How can I do it?
>
> Thanks,
>
>
> Stefano
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] R: R: Re: labels of thalami

Load them in tkmedit

On 04/28/2014 01:46 PM, std...@virgilio.it wrote:
> My apologies, but how can I visualize and check the labels obtained 
> by mri_cor2label?
>
> Thanks,
>
>
> Stefano
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 28-apr-2014 19.23
> A: 
> Ogg: [Freesurfer] R: Re: labels of thalami
>
> Thank you very much!!
>
> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 28-apr-2014 19.21
> A: 
> Ogg: Re: [Freesurfer] labels of thalami
>
>
> Use mri_cor2label
>
> On 04/28/2014 01:11 PM, std...@virgilio.it wrote:
> > Hi list,
> >
> > I'd like to obtained .labels of thalami to use it in FSL.
> >
> > How can I do it?
> >
> > Thanks,
> >
> >
> > Stefano
> >
> >
> > ___
> > 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
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Re: [Freesurfer] Coordinate transformation to average surface space


The matrix in the lta is probably not the right one. Try using 
lta_convert or tkregister2 to change it to a register.dat file (which is 
what is expected in your formula)
doug

On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
> Hi All,
>
> I am attempting to transform sets of coordinates from subject CRS 
> space into the surfaceRAS space of an average subject, made with 
> make_average_subject.
>
> By our current method, we register the individual CT to the average 
> surface using mri_robust_register with the command:
> mri_robust_register --mov  [subj_CT].img --dst average_orig.mgz --lta 
> reg_avg.lta --iscale --satit
> and then check and adjust the registration with:
> tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average
>
> These steps work fine, and when I load the average brain in freeview, 
> then load the subject CT with with the registration file reg_avg.lta 
> applied, the two overlap just as they should.
>
> However, when I attempt to do the same thing in matlab, some (though 
> not all) of the subjects present a problem.
> I do the coordinate transformation (as suggested on 
> http://freesurfer.net/fswiki/CoordinateSystems) by applying:
>
> inv(Reg_avg) * Tmov * CT_coords
>
> with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as 
> reg_avg.lta, and CT_coords as the relevant coordinates in CRS space 
> from the CT (with a vector of ones appended).
>
> As I said, some of the scans come out fine, with the coordinates in 
> the correct place on the average surface, while others are very far 
> removed from their correct location. How can I fix this?
>
> Thanks,
> Isaac
>
>
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Re: [Freesurfer] Fw: Re: convert volume-based mni152 space into fsaverage surface space(MNI305)


Try running

tkmedit fsaverage orig.mgz -reg 
$FREESURFER_HOME/average/mni152.register.dat -overlay rIPL.nii -fminmax .1 1

to see if they mask lands in the right place. If it does not, then your 
input data are not in mni152 space


On 04/25/2014 10:38 PM, charujing123 wrote:
> Hi doug,
> Thanks doug.
> I cannot see my last e-mail file in the 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/index.html#35468. 
> However I can receive it in my box, and none reply it. Maybe pitfalls 
> in the network so that you cannot read my last e-mail file. So I send 
> my last e-mail file to the freesurfer list again. Also I send to you.
> Looking forward to your new reply.
> Thanks again.
> All the best.
> Rujing Zha
> 2014-04-26
> 
> charujing123
> 
> *发件人：*"charujing123"
> *发送时间：*2014-04-25 19:22
> *主题：*Re: [Freesurfer] convert volume-based mni152 space into 
> fsaverage surface space(MNI305)
> *收件人：*"Freesurfer support list"
> *抄送：*
> Hi FS experts and users,
> Is there anyone can help me?
> Any reply will be highly appreaciated.
> Thanks.
> All the best.
> Rujing Zha
> 2014-04-25
> 
> charujing123
> 
> *发件人：*"charujing123"
> *发送时间：*2014-04-24 09:43
> *主题：*Re: [Freesurfer] convert volume-based mni152 space into 
> fsaverage surface space(MNI305)
> *收件人：*"Freesurfer support list"
> *抄送：*
> Hi doug,
> Thanks doug.
> I used this DAT file,and the command termination without any 
> problem.However the mask file dosenot overlay the rIPL area but 
> frontal area when the mask file and fsaverage file were loaded in the 
> freeview.
> Here are my scripts for creating the mask.
> mri_vol2surf --hemi rh --reg 
> $FREESURFER_HOME/average/mni152.register.dat --mov ./rIPL.nii --o 
> ./rIPL_mask.mgh --trgsubject fsaverage
> Source file volume-based mask ROI "rIPL.nii" is in the MNI152 space, 
> and two snapshot can be got in the attachment. Also registrated 
> surface ROI mask rIPL_mask.mgh snapshot can be got in the attachment.
> Here is its output in the command window.
> =
> srcvol = ./rIPL.nii
> srcreg = 
> /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/average/mni152.register.dat
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = rh
> trgsubject = fsaverage
> surfreg = sphere.reg
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> WARNING: the voxel resolution in the source volume (2,2,2) differs
>  from that listed in the registration file (1,1,1)
> Reading surface 
> /mnt/sdb1/psylab16/BACKUP/freesurfer/freesurfer/subjects/fsaverage/surf/rh.white
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>  1 0 0 0
> using old
> Done mapping volume to surface
> Number of source voxels hit = 21146
> Writing to ./rIPL_mask.mgh
> Dim: 163842 1 1
> =
> Thanks
> All the best
> Rujing Zha
> 2014-04-24
> 
> charujing123
> 
> *发件人：*Douglas N Greve 
> *发送时间：*2014-04-22 23:53
> *主题：*Re: [Freesurfer] convert volume-based mni152 space into 
> fsaverage surface space(MNI305)
> *收件人：*"freesurfer"
> *抄送：*
> Use mri_vol2surf with $FREESURFER_HOME/average/mni152.register.dat
> On 04/21/2014 10:20 PM, charujing123 wrote:
> > Hi FS experts and users,
> > I created a mask volume, whose space is in MNI152 space. And I want to
> > convert this volume into surface-based in fsaverage.
> > How can I realize this?
> > Thanks
> > All the best.
> > Rujing Zha
> > 2014-04-22
> >  
>
> > charujing123
> >
> >
> > ___
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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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>
> addressed. If you believe thi

Re: [Freesurfer] Catastrophic Surface Inaccuracies

2014-04-28 Thread Jonathan Holt

Look for spuriousWMconnections.tar 

jon
On Apr 28, 2014, at 12:03 PM, Bruce Fischl  wrote:

> sure
> On Mon, 28 Apr 2014, Jonathan Holt wrote:
> 
>> Bruce,
>> 
>> I dont see any WM connections that jump out at me. Could I upload it and 
>> have a second opinion?
>> 
>> Jon
>> On Apr 25, 2014, at 11:33 PM, Bruce Fischl  
>> wrote:
>> 
>>> Hi Jon
>>> 
>>> in this kind of case the default method did the wrong thing (closing the 
>>> hole instead of cutting the handle). You need to identify the incorrectly 
>>> segmented voxels that cause the spurious correction and delete them from 
>>> the wm.mgz, then run autorecon2-wm autorecon3
>>> 
>>> cheers
>>> Bruce
>>> 
>>> 
>>> On Fri, 25 Apr 2014, Jonathan Holt wrote:
>>> 
 Thanks Bruce,
 
 I’ll check for such wm connections. Is this the default method for 
 correcting topology issues?
 
 jon
 On Apr 25, 2014, at 10:59 PM, Bruce Fischl  
 wrote:
 
> Hi Jon
> 
> that is almost certainly a topology correction problem. Check to see if 
> the wm.mgz contains any spurious connections that cause the space that is 
> missing in the ?h.white surface to be closed in a slice. If you upload 
> the data we can show you how to correct it if you want.
> 
> cheers
> Bruce
> On Fri, 25 Apr 2014, Jonathan Holt wrote:
> 
>> Hi all,
>> I would love information on how best to tackle and alleviate this type 
>> of surface issue. Images
>> attached.
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>> 
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Re: [Freesurfer] incongruent coordinates in freeview and *sig.cluster.summary


On 04/26/2014 07:06 AM, charujing123 wrote:
> Hi all,
> I have done group analysis and see it in freeview. Also I can see my 
> sig.cluster.summary file to find clusters those survived. As I know, 
> the MNIX MNIY MNIZ in the cluster summary file is coordinates for the 
> maximum. The coordinate system is MNI305. Also I input the vertex 
> number at the maximum in freeview, but it echo different coordinate 
> for the vertex from that in cluster summary file. Why?
Which coordinate? are you looking at and on which surface?
> Another question. There is "RAS" symbol at the bottom of freeview 
> window. However I see the coordinates : inferior, posterior, left is 
> negtive, superior, anterior,and right is positive. I suspect the 
> coordinate system is LPI. Is that right?
If left is negative, then it is RAS
> Thanks.
> All the best.
> Rujing Zha
> 2014-04-26
> 
> charujing123
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] Question about visualization on the surface


On 04/26/2014 02:54 PM, Kaveh Kohan wrote:
> Dear All,
>
> This probably a newbie question, so I apologize if it is a naive one, 
> please bear with me.
>
> I have on value for each ROI on the surface of brain and one value for 
> each sub-cortical structures.  Those ROIs and sub-cortical structures 
> correspond to freesurfer atlas.
>
> I have three questions:
>
> * I am not sure which freesurfer ATLAS these values correspond to? Is 
> there any way to tell from the name of structures? I have attached two 
> text files including the header of the tables.
The aseg corresponds to the RB_all_2008-03-26.gca (see Fischl's 2002(?) 
Neuron paper), the other corresponds to the Desikan/Killiany atlas.
>
> * How can I visualize those values on the inflated brain? Something 
> like this:
>
> http://pysurfer.github.io/examples/plot_parc_values.html
>
> This package is a great but unfortunately very unstable (at least on 
> my laptop). It visualizes the brain but crashes immediately! No time 
> to save the results. Is there any MATLAB equivalent?
>
> * What is the best way to visualize the values for the subcortical 
> structures?
We don't have a good way to get ROI values back into the volume or the 
surface. I'd probably do it in matlab
doug
>
> Any comment is highly appreciated,
>
> Again, I am sorry if those are naive questions.
>
> Thanks,
>
>
>
>
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Re: [Freesurfer] Coordinate transformation to average surface space

2014-04-28 Thread Martin Reuter

Also robust register (at least the standard version that you use) is not 
designed to do cross modal registration. So I am amazed it can register 
a CT to an MRI at all (if that is what you are doing). To get a better 
registration try
- using a different cost functions, e.g.
--cost nmi   (normalized mutual information)

Also you could try using bb_register if you have surfaces on the mri.

Best, Martin

On 04/28/2014 02:32 PM, Douglas N Greve wrote:
> The matrix in the lta is probably not the right one. Try using
> lta_convert or tkregister2 to change it to a register.dat file (which is
> what is expected in your formula)
> doug
>
> On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
>> Hi All,
>>
>> I am attempting to transform sets of coordinates from subject CRS
>> space into the surfaceRAS space of an average subject, made with
>> make_average_subject.
>>
>> By our current method, we register the individual CT to the average
>> surface using mri_robust_register with the command:
>> mri_robust_register --mov  [subj_CT].img --dst average_orig.mgz --lta
>> reg_avg.lta --iscale --satit
>> and then check and adjust the registration with:
>> tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average
>>
>> These steps work fine, and when I load the average brain in freeview,
>> then load the subject CT with with the registration file reg_avg.lta
>> applied, the two overlap just as they should.
>>
>> However, when I attempt to do the same thing in matlab, some (though
>> not all) of the subjects present a problem.
>> I do the coordinate transformation (as suggested on
>> http://freesurfer.net/fswiki/CoordinateSystems) by applying:
>>
>> inv(Reg_avg) * Tmov * CT_coords
>>
>> with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as
>> reg_avg.lta, and CT_coords as the relevant coordinates in CRS space
>> from the CT (with a vector of ones appended).
>>
>> As I said, some of the scans come out fine, with the coordinates in
>> the correct place on the average surface, while others are very far
>> removed from their correct location. How can I fix this?
>>
>> Thanks,
>> Isaac
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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Instructor in Neurology
   Harvard Medical School
Assistant in Neuroscience
   Dept. of Radiology, Massachusetts General Hospital
   Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
   Computer Science and Artificial Intelligence Lab,
   Dept. of Electrical Engineering and Computer Science,
   Massachusetts Institute of Technology

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Re: [Freesurfer] Extract ROI from anatomical volume

2014-04-28 Thread pfotiad

Hi Bruce,

Yes, that's exactly what I needed, thanks a lot!

Best,
Panos


> Hi Panos
>
> so you want an intensity volume that is zero everywhere except in a
> label? If so, try mri_mask
>
> cheers
> Bruce
>
> On Mon, 28 Apr 2014, pfot...@nmr.mgh.harvard.edu wrote:
>
>> Hi FS experts,
>>
>> I was wondering what the best way to extract an ROI from an anatomical
>> volume would be. For instance, I would like to create a volume of only
>> the
>> wm-lh-precentral based on the orig.mgz volume and on the segmentation
>> map
>> wmparc.mgz. I know that something similar can be done with the
>> mri_extract_label command, but if I'm not mistaken that command can only
>> be applied to a segmentation volume, and not on an anatomical volume
>> like
>> orig.mgz.
>>
>> Thanks in advance,
>> Panos
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>>
>>
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>
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Re: [Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?

There should be a ?h.volume file. Are you sure there is not? You can 
specify -meas volume when you run mris_preproc
doug

On 04/27/2014 08:35 PM, Yizhou Ma wrote:
> Dear freesurfer experts,
>
> I am working on a project on cortical asymmetry and I have analyzed 
> vertex-wise cortical thickness/surface area asymmetry. However, I 
> noticed that Freesurfer doesn't not seem to facilitate such analysis 
> for gray matter volume, as after running surfreg -xhemi there is no 
> ?h.volume file in subject/xhemi/surf. I searched the literature and 
> found studies on gray matter density asymmetry with VBM and ROI-based 
> volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise 
> volume asymmetry analysis? And may I know the rationale?
>
> Thanks,
> Cherry
>
>
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Re: [Freesurfer] Coordinate transformation to average surface space

2014-04-28 Thread ISAAC PEDISICH

Hi Doug,
Thanks for the response.
I'm not seeing lta_convert as an executable that I can run. I have
freesurfer v5.3.0 installed - is there another version that I should be
using?

For using tkregister2, I'm a bit confused as to what I should be doing. I
had assumed (erroneously, it seems) that the .lta and .dat files contained
the same information.
I just tried re-running tkregister2 with the command:
tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s average
--lta reg_avg.lta
Such that I can pass in the reg_avg.lta file created from robust register,
and have it output a reg_avg.dat file. The contents of these two files,
however, seem to be exactly the same.

I also running  tkregister2 with the --fslregout and --freeview flags, but
neither of those produced a correct transformation either.

Martin:
We are indeed registering the CT to an average MRI, and for the moment we
are correcting inaccuracies manually with tkregister2.
I just tried bbregister with one of our problem subjects, and it still
produced a matrix that had to be significantly adjusted in tkregister2.
Furthermore, the matrix that it produced still did not transform the
coordinates correctly in MATLAB.

-Isaac


On Mon, Apr 28, 2014 at 2:32 PM, Douglas N Greve
wrote:

>
> The matrix in the lta is probably not the right one. Try using
> lta_convert or tkregister2 to change it to a register.dat file (which is
> what is expected in your formula)
> doug
>
> On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
> > Hi All,
> >
> > I am attempting to transform sets of coordinates from subject CRS
> > space into the surfaceRAS space of an average subject, made with
> > make_average_subject.
> >
> > By our current method, we register the individual CT to the average
> > surface using mri_robust_register with the command:
> > mri_robust_register --mov  [subj_CT].img --dst average_orig.mgz --lta
> > reg_avg.lta --iscale --satit
> > and then check and adjust the registration with:
> > tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average
> >
> > These steps work fine, and when I load the average brain in freeview,
> > then load the subject CT with with the registration file reg_avg.lta
> > applied, the two overlap just as they should.
> >
> > However, when I attempt to do the same thing in matlab, some (though
> > not all) of the subjects present a problem.
> > I do the coordinate transformation (as suggested on
> > http://freesurfer.net/fswiki/CoordinateSystems) by applying:
> >
> > inv(Reg_avg) * Tmov * CT_coords
> >
> > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as
> > reg_avg.lta, and CT_coords as the relevant coordinates in CRS space
> > from the CT (with a vector of ones appended).
> >
> > As I said, some of the scans come out fine, with the coordinates in
> > the correct place on the average surface, while others are very far
> > removed from their correct location. How can I fix this?
> >
> > Thanks,
> > Isaac
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Re: [Freesurfer] Coordinate transformation to average surface space


FYI, it is bbregister not bb_register :-)


On 04/28/2014 02:51 PM, Martin Reuter wrote:
> Also robust register (at least the standard version that you use) is not
> designed to do cross modal registration. So I am amazed it can register
> a CT to an MRI at all (if that is what you are doing). To get a better
> registration try
> - using a different cost functions, e.g.
> --cost nmi   (normalized mutual information)
>
> Also you could try using bb_register if you have surfaces on the mri.
>
> Best, Martin
>
> On 04/28/2014 02:32 PM, Douglas N Greve wrote:
>> The matrix in the lta is probably not the right one. Try using
>> lta_convert or tkregister2 to change it to a register.dat file (which is
>> what is expected in your formula)
>> doug
>>
>> On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
>>> Hi All,
>>>
>>> I am attempting to transform sets of coordinates from subject CRS
>>> space into the surfaceRAS space of an average subject, made with
>>> make_average_subject.
>>>
>>> By our current method, we register the individual CT to the average
>>> surface using mri_robust_register with the command:
>>> mri_robust_register --mov  [subj_CT].img --dst average_orig.mgz --lta
>>> reg_avg.lta --iscale --satit
>>> and then check and adjust the registration with:
>>> tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial --s average
>>>
>>> These steps work fine, and when I load the average brain in freeview,
>>> then load the subject CT with with the registration file reg_avg.lta
>>> applied, the two overlap just as they should.
>>>
>>> However, when I attempt to do the same thing in matlab, some (though
>>> not all) of the subjects present a problem.
>>> I do the coordinate transformation (as suggested on
>>> http://freesurfer.net/fswiki/CoordinateSystems) by applying:
>>>
>>> inv(Reg_avg) * Tmov * CT_coords
>>>
>>> with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as
>>> reg_avg.lta, and CT_coords as the relevant coordinates in CRS space
>>> from the CT (with a vector of ones appended).
>>>
>>> As I said, some of the scans come out fine, with the coordinates in
>>> the correct place on the average surface, while others are very far
>>> removed from their correct location. How can I fix this?
>>>
>>> Thanks,
>>> Isaac
>>>
>>>
>>> ___
>>> 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
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Re: [Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?

2014-04-28 Thread Yizhou Ma

Thanks Doug. I have ?h.volume in subject/surf but not in
subject/xhemi/surf. I followed this page
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a problem
with surfreg rather than mris_preproc. Can I just copy the ?h.volume from
subject/surf to subject/xhemi/surf?

Best,
Cherry


On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve
wrote:

>
>
> There should be a ?h.volume file. Are you sure there is not? You can
> specify -meas volume when you run mris_preproc
> doug
>
> On 04/27/2014 08:35 PM, Yizhou Ma wrote:
> > Dear freesurfer experts,
> >
> > I am working on a project on cortical asymmetry and I have analyzed
> > vertex-wise cortical thickness/surface area asymmetry. However, I
> > noticed that Freesurfer doesn't not seem to facilitate such analysis
> > for gray matter volume, as after running surfreg -xhemi there is no
> > ?h.volume file in subject/xhemi/surf. I searched the literature and
> > found studies on gray matter density asymmetry with VBM and ROI-based
> > volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise
> > volume asymmetry analysis? And may I know the rationale?
> >
> > Thanks,
> > Cherry
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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>
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Re: [Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?


Then something went wrong along the way. Check the xhemi/xhemireg.?h.log 
to see if there is an error. If not, send the log file to me

On 04/28/2014 04:14 PM, Yizhou Ma wrote:
> Thanks Doug. I have ?h.volume in subject/surf but not in 
> subject/xhemi/surf. I followed this page 
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a 
> problem with surfreg rather than mris_preproc. Can I just copy the 
> ?h.volume from subject/surf to subject/xhemi/surf?
>
> Best,
> Cherry
>
>
> On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
>
> There should be a ?h.volume file. Are you sure there is not? You can
> specify -meas volume when you run mris_preproc
> doug
>
> On 04/27/2014 08:35 PM, Yizhou Ma wrote:
> > Dear freesurfer experts,
> >
> > I am working on a project on cortical asymmetry and I have analyzed
> > vertex-wise cortical thickness/surface area asymmetry. However, I
> > noticed that Freesurfer doesn't not seem to facilitate such analysis
> > for gray matter volume, as after running surfreg -xhemi there is no
> > ?h.volume file in subject/xhemi/surf. I searched the literature and
> > found studies on gray matter density asymmetry with VBM and
> ROI-based
> > volume asymmetry. Is it true that Freesurfer doesn't offer
> vertex-wise
> > volume asymmetry analysis? And may I know the rationale?
> >
> > Thanks,
> > Cherry
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Coordinate transformation to average surface space


When you say the content is the same, do you mean exactly the same or 
just the matrix? Also, what coordinate system are you trying to go to? 
The equation you have below takes CRS in the CT and maps it to tkrRAS in 
the anatomical. If you want to map the CRS in the anat then use

inv(Tanat) * inv(Reg_avg) * Tmov * CT_coords


On 04/28/2014 03:58 PM, ISAAC PEDISICH wrote:
> Hi Doug,
> Thanks for the response.
> I'm not seeing lta_convert as an executable that I can run. I have 
> freesurfer v5.3.0 installed - is there another version that I should 
> be using?
>
> For using tkregister2, I'm a bit confused as to what I should be 
> doing. I had assumed (erroneously, it seems) that the .lta and .dat 
> files contained the same information.
> I just tried re-running tkregister2 with the command:
> tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s 
> average --lta reg_avg.lta
> Such that I can pass in the reg_avg.lta file created from robust 
> register, and have it output a reg_avg.dat file. The contents of these 
> two files, however, seem to be exactly the same.
>
> I also running  tkregister2 with the --fslregout and --freeview flags, 
> but neither of those produced a correct transformation either.
>
> Martin:
> We are indeed registering the CT to an average MRI, and for the moment 
> we are correcting inaccuracies manually with tkregister2.
> I just tried bbregister with one of our problem subjects, and it still 
> produced a matrix that had to be significantly adjusted in 
> tkregister2. Furthermore, the matrix that it produced still did not 
> transform the coordinates correctly in MATLAB.
>
> -Isaac
>
>
> On Mon, Apr 28, 2014 at 2:32 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> The matrix in the lta is probably not the right one. Try using
> lta_convert or tkregister2 to change it to a register.dat file
> (which is
> what is expected in your formula)
> doug
>
> On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
> > Hi All,
> >
> > I am attempting to transform sets of coordinates from subject CRS
> > space into the surfaceRAS space of an average subject, made with
> > make_average_subject.
> >
> > By our current method, we register the individual CT to the average
> > surface using mri_robust_register with the command:
> > mri_robust_register --mov  [subj_CT].img --dst average_orig.mgz
> --lta
> > reg_avg.lta --iscale --satit
> > and then check and adjust the registration with:
> > tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial
> --s average
> >
> > These steps work fine, and when I load the average brain in
> freeview,
> > then load the subject CT with with the registration file reg_avg.lta
> > applied, the two overlap just as they should.
> >
> > However, when I attempt to do the same thing in matlab, some (though
> > not all) of the subjects present a problem.
> > I do the coordinate transformation (as suggested on
> > http://freesurfer.net/fswiki/CoordinateSystems) by applying:
> >
> > inv(Reg_avg) * Tmov * CT_coords
> >
> > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as
> > reg_avg.lta, and CT_coords as the relevant coordinates in CRS space
> > from the CT (with a vector of ones appended).
> >
> > As I said, some of the scans come out fine, with the coordinates in
> > the correct place on the average surface, while others are very far
> > removed from their correct location. How can I fix this?
> >
> > Thanks,
> > Isaac
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners

Re: [Freesurfer] Coordinate transformation to average surface space

2014-04-28 Thread ISAAC PEDISICH

Sorry - I meant just the matrix.

I'm trying to map from CRS in the CT to tkrRAS in the anatomical, I
believe. I'm a little unclear as to what exactly anat space means, but I
know that I'm trying to get it from CRS in the CT to the space in which the
surface is plotted in MATLAB, which I believe is tkrRAS, anatomical. I'm
certain it's no longer CRS space, as the x-coordinates must contain some
negative indices.



On Mon, Apr 28, 2014 at 5:02 PM, Douglas N Greve
wrote:

>
> When you say the content is the same, do you mean exactly the same or
> just the matrix? Also, what coordinate system are you trying to go to?
> The equation you have below takes CRS in the CT and maps it to tkrRAS in
> the anatomical. If you want to map the CRS in the anat then use
>
> inv(Tanat) * inv(Reg_avg) * Tmov * CT_coords
>
>
> On 04/28/2014 03:58 PM, ISAAC PEDISICH wrote:
> > Hi Doug,
> > Thanks for the response.
> > I'm not seeing lta_convert as an executable that I can run. I have
> > freesurfer v5.3.0 installed - is there another version that I should
> > be using?
> >
> > For using tkregister2, I'm a bit confused as to what I should be
> > doing. I had assumed (erroneously, it seems) that the .lta and .dat
> > files contained the same information.
> > I just tried re-running tkregister2 with the command:
> > tkregsiter2 --mov [sub_CT].img --reg reg_avg.dat --surf pial --s
> > average --lta reg_avg.lta
> > Such that I can pass in the reg_avg.lta file created from robust
> > register, and have it output a reg_avg.dat file. The contents of these
> > two files, however, seem to be exactly the same.
> >
> > I also running  tkregister2 with the --fslregout and --freeview flags,
> > but neither of those produced a correct transformation either.
> >
> > Martin:
> > We are indeed registering the CT to an average MRI, and for the moment
> > we are correcting inaccuracies manually with tkregister2.
> > I just tried bbregister with one of our problem subjects, and it still
> > produced a matrix that had to be significantly adjusted in
> > tkregister2. Furthermore, the matrix that it produced still did not
> > transform the coordinates correctly in MATLAB.
> >
> > -Isaac
> >
> >
> > On Mon, Apr 28, 2014 at 2:32 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > The matrix in the lta is probably not the right one. Try using
> > lta_convert or tkregister2 to change it to a register.dat file
> > (which is
> > what is expected in your formula)
> > doug
> >
> > On 04/25/2014 12:28 PM, ISAAC PEDISICH wrote:
> > > Hi All,
> > >
> > > I am attempting to transform sets of coordinates from subject CRS
> > > space into the surfaceRAS space of an average subject, made with
> > > make_average_subject.
> > >
> > > By our current method, we register the individual CT to the average
> > > surface using mri_robust_register with the command:
> > > mri_robust_register --mov  [subj_CT].img --dst average_orig.mgz
> > --lta
> > > reg_avg.lta --iscale --satit
> > > and then check and adjust the registration with:
> > > tkregister2 --mov [subj_CT].img --reg reg_avg.lta --surf pial
> > --s average
> > >
> > > These steps work fine, and when I load the average brain in
> > freeview,
> > > then load the subject CT with with the registration file
> reg_avg.lta
> > > applied, the two overlap just as they should.
> > >
> > > However, when I attempt to do the same thing in matlab, some
> (though
> > > not all) of the subjects present a problem.
> > > I do the coordinate transformation (as suggested on
> > > http://freesurfer.net/fswiki/CoordinateSystems) by applying:
> > >
> > > inv(Reg_avg) * Tmov * CT_coords
> > >
> > > with Tmov: mri_info --vox2ras-tkr [subj_CT].img, Reg_avg as
> > > reg_avg.lta, and CT_coords as the relevant coordinates in CRS space
> > > from the CT (with a vector of ones appended).
> > >
> > > As I said, some of the scans come out fine, with the coordinates in
> > > the correct place on the average surface, while others are very far
> > > removed from their correct location. How can I fix this?
> > >
> > > Thanks,
> > > Isaac
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> >

Re: [Freesurfer] repost: mri_convert Siemens Skyra .IMA CentOS5.7 FS5.3