Re: [Freesurfer] CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference

[Hemant Bokil]

HI Richard,
Thanks for the response. Does this mean that I should use CUDA 3.2 ? There
was some discussion on the group recently about Freesurfer not working with
CUDA 4 and one suggestion made was to switch to CUDA 3.2. Thanks,
Hemant

On Mon, Oct 24, 2011 at 7:07 PM, R Edgar  wrote:

> On Mon, Oct 24, 2011 at 3:36 PM, Hemant Bokil 
> wrote:
>
> > Driver : 4.10
> > Runtime : 3.20
>
> My best guess would be this mismatch causing a problem. It shouldn't
> in theory, but...
>
> Richard
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Re: [Freesurfer] CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference

[R Edgar]

On Mon, Oct 24, 2011 at 3:36 PM, Hemant Bokil  wrote:

> Driver : 4.10
> Runtime : 3.20

My best guess would be this mismatch causing a problem. It shouldn't
in theory, but...

Richard
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Re: [Freesurfer] mris_anatomical stats different thickness files

[Douglas N Greve]

no, that would be 15 "smooth steps". If you want to smooth by 15mm, then 
use mris_fwhm.
doug

krista kelly wrote:
> Would the following code give me data smoothed with 15 fwhm kernel?
>
> mris_anatomical_stats -l lh.v1.label -t lh.thickness -nsmooth 15 -b -f 
> BV01/stats/lh.v1_pial.stats BV01 lh pial
>
>
> Thanks!
>
>
> On Mon, Oct 24, 2011 at 10:40 AM, krista kelly 
> mailto:krista.kell...@gmail.com>> wrote:
>
> Thanks for clearing this up! It makes a lot more sense now.
>
>
> On Mon, Oct 24, 2011 at 10:35 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
>
> krista kelly wrote:
>
> I'm looking at both cortical thickness and surface area
> differences between two groups. I've been using
> mris_anatomical_stats to retrieve values but had a few
> questions:
>
> 1) Do I need to do separate mris_anatomical_stats using
> different thickness files (bolded below) to get cortical
> thickness and surface area measures. For example:
>
> cortical thickness - mris_anatomical_stats -l lh.v1.label
> -t *lh.thickness* -b -f BV01/stats/lh.v1.stats BV01 lh
> surface area - mris_anatomical_stats -l lh.v1.label -t
> *lh.area *-b -f BV01/stats/lh.v1.stats BV01 lh
>
>
>  Or, since the output files include all of these measures,
> is it fine to just run one of the two?
>
> Just run the first one.
>
>
> 2) The output files for both analyses run above (with
> different thickness files) have identical values for
> everything except for tray matter volume. Using
> lh.thickness file - grayvol = 8082; using lh.area file -
> grayvol = 4029. Can anyone clarify why this happens?
>
> It computes the gray matter volume by thickness*area. If you
> pass it "area" as the "thickness", then you are probably
> getting area*area. Though I'm surprised that the "thickness"
> values are correct.
>
>
> 3) The default surface area values are for the white
> matter surface. How do I run mri_anatomical_stats to get
> the pial surface? I've tried mris_anatomical_stats -l
> lh.v1.label -t *lh.area.pial *-b -f BV01/stats/lh.v1.stats
> BV01 lh but I get identical values for everything (except
> grayvol).
>
> Try adding "pial" to the end of the command line (and use
> lh.thickness)
> doug
>
>
> Thanks!
> Krista
> 
> 
>
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>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358  Fax:
> 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
>
>
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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

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Re: [Freesurfer] white matter volume in a ROI

[Douglas N Greve]

It will be more involved than that. You will need to create an 
annotation that contains your label (maybe in addition to other labels), 
then uses mri_aparc2aseg with the --labelwm option, something like

mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown 
--volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot

doug

dolphin...@aol.com wrote:
> Hi Doug,
>
> thanks a lot for your answer.
>
> So i understand you right that i can get "exact" knowledge about the 
> thickness, grey matter volume and pial surface area in my ROI, but in 
> case of "the" ROI white matter volume, i have to look to which 
> cortical label my ROI counts and then I use the wmparc.files for this 
> label?
>
> Best regards
>
> Daniel Klein
>
>
>
>  
>
>
>
>
>
> -Ursprüngliche Mitteilung-
> Von: Douglas N Greve 
> An: dolphinede 
> Cc: freesurfer 
> Verschickt: Mo, 24 Okt 2011 4:48 pm
> Betreff: Re: [Freesurfer] white matter volume in a ROI
>
> For GM area and volume, you can use mris_anatomical_stats. See the 
> recent thread on how. For the WM volume, how would you define the WM 
> volume that corresponds to you label? We have a routine that parcellates 
> WM based on closest proximity to a cortical label.
> doug
>
> dolphin...@aol.com wrote:
> > Dear FreeSurfer experts,
> >
> > i have created  a ROI in qdec  , where i have found a significant 
> > correlation between lgi and age.
> >
> > I mapped this ROI to all subjects.
> >
> > I am interested to compare in this ROI the pial-surface area, the grey 
> > matter volume and if possible the white matter volume for this 
> > specific region and i am not sure how to do this?
> >
> > Best regards
> >
> > Daniel Klein
> > 
> >
> > ___
> > 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
>
>
>
> 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
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[Freesurfer] CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line 92 : invalid texture reference

[Hemant Bokil]

Hi all,
Here are the details of my freesurfer and linux installations

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

RedHat release: CentOS Linux release 6.0 (Final)

Kernel info: Linux 2.6.32-71.29.1.el6.x86_64 x86_64

I successfully ran autorecon2 without gpu on several datasets that we have.
However, when I try to use the GPU, I get the following error message:
CUDA Error in file
'/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line
92 : invalid texture reference

The calling sequence and all on-screen messages are listed at the end of
this email. A similar error was reported a year ago by a different user (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-August/015528.html)
so I am hoping there is a simple fix. Thanks in advance,
Hemant


recon-all -subjid 203 -use-gpu -autorecon2
Testing for CUDA device:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2010 NVIDIA Corporation
Built on Thu_Nov__4_12:44:17_PDT_2010
Cuda compilation tools, release 3.2, V0.2.1221

Driver : 4.10
Runtime : 3.20

Acquiring CUDA device
Using default device
CUDA device: Quadro FX 4600
stable5

NVIDIA driver version info:
NVRM version: NVIDIA UNIX x86_64 Kernel Module  285.05.09  Fri Sep 23
17:31:57 PDT 2011

Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /home/hemant/FreeSurferSubjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r--. 1 hemant hemant 226454 Oct 24 15:05
/home/hemant/FreeSurferSubjects/203/scripts/recon-all.log
Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27
19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux
#-
#@# EM Registration Mon Oct 24 15:05:52 EDT 2011
/home/hemant/FreeSurferSubjects/203/mri

 mri_em_register_cuda -uns 3 -mask brainmask.mgz nu.mgz
/usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta


nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2010 NVIDIA Corporation
Built on Thu_Nov__4_12:44:17_PDT_2010
Cuda compilation tools, release 3.2, V0.2.1221

Driver : 4.10
Runtime : 3.20

Acquiring CUDA device
Using default device
CUDA device: Quadro FX 4600
aligning to atlas containing skull, setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'...
gcaAllocMax: node dims 64 64 64
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
average std = 6.9   using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 14.9 or > 790.2
total sample mean = 84.4 (994 zeros)

spacing=8, using 2772 sample points, tol=1.00e-05...

CUDA Error in file
'/space/freesurfer/build/minerva/stable/dev/include/ctfactory.hpp' on line
92 : invalid texture reference.
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2772, passno 0, spacing 8
Abort (core dumped)
Linux Lab-3.intelect.local 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27
19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 203 exited with ERRORS at Mon Oct 24 15:06:11 EDT 2011
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Re: [Freesurfer] implementation on Neurodebian

[Bruce Fischl]

just CUDA for now.

Bruce
On Mon, 24 Oct 2011, Cartik Sharma wrote:

> Bruce,
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide#Benchmarks
> Found this link..clearly impressive, are these benchmarks for GPU enabled
> cards with CUDA or also with ATI Radeon GPU enabled cards?
>
> Best,
> Cartik
>
> On Oct 24, 2011, at 10:30 AM, Bruce Fischl wrote:
>
>> not yet, although it is something we are working on.
>>
>> cheers
>> Bruce
>> On Mon, 24 Oct 2011, Cartik Sharma wrote:
>>
>>> Hi Knut,
>>> Good to know we can speed things up with CUDA. I have a multicore CPU and 
>>> was wondering if
>>> there is a parallelized version of Freesurfer on the CPU.
>>> Thanks for the speedup!
>>> Best regards,
>>> Cartik
>>> On Oct 24, 2011, at 4:41 AM, Knut J Bjuland wrote:
>>>
>>>  Hi Cartik
>>>
>>>  You use -use-gpu to offload rendering to the GPU using cuda.
>>>
>>>  Knut J
>>>
>>> > From: cartik.sha...@childmind.org
>>> > To: knut...@hotmail.com
>>> > Subject: Re: [Freesurfer] implementation on Neurodebian
>>> > Date: Thu, 20 Oct 2011 15:48:10 +
>>> >
>>> > Hi Knut:
>>> >
>>> > Cool..is this speeding up things by rendering on the GPU.
>>> > Is there a way to offload computation to the GPU.
>>> >
>>> > Best regards,
>>> > Cartik
>>> >
>>> > On Oct 20, 2011, at 10:57 AM, Knut J Bjuland wrote:
>>> >
>>> >> Hi Cartik
>>> >>
>>> >> If you enable cuda with -use-gpu the recon-all will run faster.
>>> >>
>>> >> Knut J
>>> >>
>>> >> Den 17.10.2011 16:41, skrev Cartik Sharma:
>>> >>> Dear Freesurfer developer(s),
>>> >>>
>>> >>> Is there a way to get Freesurfer run faster on Neurodebian. While 
>>> the package produces
>>> >>> some truly out of the world segmentations and labels for the 
>>> cortical surface, it seems
>>> >>> to take time.
>>> >>>
>>> >>> For eg:
>>> >>> Defect correction and retesellation takes an hour, other steps take 
>>> longer..I'm not sure if
>>> >>> it's the original dataset, the OS platform (i.e Virtual Machine, 
>>> Neurodebian) or original
>>> >>> computational engine itself.
>>> >>>
>>> >>> Would be happy in efforts and hints to make this run faster.
>>> >>>
>>> >>> Best regards,
>>> >>> Cartik Sharma
>>> >>>
>>> >>>
>>> >>> ___
>>> >>> Freesurfer mailing list
>>> >>> Freesurfer@nmr.mgh.harvard.edu
>>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >>>
>>> >>>
>>> >>> The information in this e-mail is intended only for the person to 
>>> whom it is
>>> >>> addressed. If you believe this e-mail was sent to you in error and 
>>> the e-mail
>>> >>> contains patient information, please contact the Partners 
>>> Compliance HelpLine at
>>> >>> http://www.partners.org/complianceline . If the e-mail was sent to 
>>> you in error
>>> >>> but does not contain patient information, please contact the sender 
>>> and properly
>>> >>> dispose of the e-mail.
>>> >>>
>>> >>>
>>> >>>
>>> >>
>>> >
>
>
>
>
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Re: [Freesurfer] implementation on Neurodebian

[Pedro Paulo de Magalhães Oliveira Junior]

No. Cuda only runs in NVidia hardware.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441




On Mon, Oct 24, 2011 at 13:01, Cartik Sharma wrote:

> Bruce,
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide#Benchmarks
> Found this link..clearly impressive, are these benchmarks for GPU enabled
> cards with CUDA or also with ATI Radeon GPU enabled cards?
>
> Best,
> Cartik
>
> On Oct 24, 2011, at 10:30 AM, Bruce Fischl wrote:
>
> > not yet, although it is something we are working on.
> >
> > cheers
> > Bruce
> > On Mon, 24 Oct 2011, Cartik Sharma wrote:
> >
> >> Hi Knut,
> >> Good to know we can speed things up with CUDA. I have a multicore CPU
> and was wondering if
> >> there is a parallelized version of Freesurfer on the CPU.
> >> Thanks for the speedup!
> >> Best regards,
> >> Cartik
> >> On Oct 24, 2011, at 4:41 AM, Knut J Bjuland wrote:
> >>
> >>  Hi Cartik
> >>
> >>  You use -use-gpu to offload rendering to the GPU using cuda.
> >>
> >>  Knut J
> >>
> >>  > From: cartik.sha...@childmind.org
> >>  > To: knut...@hotmail.com
> >>  > Subject: Re: [Freesurfer] implementation on Neurodebian
> >>  > Date: Thu, 20 Oct 2011 15:48:10 +
> >>  >
> >>  > Hi Knut:
> >>  >
> >>  > Cool..is this speeding up things by rendering on the GPU.
> >>  > Is there a way to offload computation to the GPU.
> >>  >
> >>  > Best regards,
> >>  > Cartik
> >>  >
> >>  > On Oct 20, 2011, at 10:57 AM, Knut J Bjuland wrote:
> >>  >
> >>  > > Hi Cartik
> >>  > >
> >>  > > If you enable cuda with -use-gpu the recon-all will run faster.
> >>  > >
> >>  > > Knut J
> >>  > >
> >>  > > Den 17.10.2011 16:41, skrev Cartik Sharma:
> >>  > >> Dear Freesurfer developer(s),
> >>  > >>
> >>  > >> Is there a way to get Freesurfer run faster on Neurodebian.
> While the package produces
> >>  > >> some truly out of the world segmentations and labels for the
> cortical surface, it seems
> >>  > >> to take time.
> >>  > >>
> >>  > >> For eg:
> >>  > >> Defect correction and retesellation takes an hour, other steps
> take longer..I'm not sure if
> >>  > >> it's the original dataset, the OS platform (i.e Virtual
> Machine, Neurodebian) or original
> >>  > >> computational engine itself.
> >>  > >>
> >>  > >> Would be happy in efforts and hints to make this run faster.
> >>  > >>
> >>  > >> Best regards,
> >>  > >> Cartik Sharma
> >>  > >>
> >>  > >>
> >>  > >> ___
> >>  > >> Freesurfer mailing list
> >>  > >> Freesurfer@nmr.mgh.harvard.edu
> >>  > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>  > >>
> >>  > >>
> >>  > >> The information in this e-mail is intended only for the person
> to whom it is
> >>  > >> addressed. If you believe this e-mail was sent to you in error
> and the e-mail
> >>  > >> contains patient information, please contact the Partners
> Compliance HelpLine at
> >>  > >> http://www.partners.org/complianceline . If the e-mail was
> sent to you in error
> >>  > >> but does not contain patient information, please contact the
> sender and properly
> >>  > >> dispose of the e-mail.
> >>  > >>
> >>  > >>
> >>  > >>
> >>  > >
> >>  >
>
>
> ___
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Re: [Freesurfer] implementation on Neurodebian

[Cartik Sharma]

Bruce,

http://surfer.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide#Benchmarks
Found this link..clearly impressive, are these benchmarks for GPU enabled
cards with CUDA or also with ATI Radeon GPU enabled cards?

Best,
Cartik

On Oct 24, 2011, at 10:30 AM, Bruce Fischl wrote:

> not yet, although it is something we are working on.
> 
> cheers
> Bruce
> On Mon, 24 Oct 2011, Cartik Sharma wrote:
> 
>> Hi Knut,
>> Good to know we can speed things up with CUDA. I have a multicore CPU and 
>> was wondering if
>> there is a parallelized version of Freesurfer on the CPU.
>> Thanks for the speedup!
>> Best regards,
>> Cartik
>> On Oct 24, 2011, at 4:41 AM, Knut J Bjuland wrote:
>> 
>>  Hi Cartik
>> 
>>  You use -use-gpu to offload rendering to the GPU using cuda. 
>> 
>>  Knut J
>> 
>>  > From: cartik.sha...@childmind.org
>>  > To: knut...@hotmail.com
>>  > Subject: Re: [Freesurfer] implementation on Neurodebian
>>  > Date: Thu, 20 Oct 2011 15:48:10 +
>>  > 
>>  > Hi Knut:
>>  > 
>>  > Cool..is this speeding up things by rendering on the GPU.
>>  > Is there a way to offload computation to the GPU.
>>  > 
>>  > Best regards,
>>  > Cartik
>>  > 
>>  > On Oct 20, 2011, at 10:57 AM, Knut J Bjuland wrote:
>>  > 
>>  > > Hi Cartik
>>  > > 
>>  > > If you enable cuda with -use-gpu the recon-all will run faster.
>>  > > 
>>  > > Knut J
>>  > > 
>>  > > Den 17.10.2011 16:41, skrev Cartik Sharma:
>>  > >> Dear Freesurfer developer(s),
>>  > >> 
>>  > >> Is there a way to get Freesurfer run faster on Neurodebian. While 
>> the package produces
>>  > >> some truly out of the world segmentations and labels for the 
>> cortical surface, it seems
>>  > >> to take time.
>>  > >> 
>>  > >> For eg:
>>  > >> Defect correction and retesellation takes an hour, other steps 
>> take longer..I'm not sure if
>>  > >> it's the original dataset, the OS platform (i.e Virtual Machine, 
>> Neurodebian) or original
>>  > >> computational engine itself.
>>  > >> 
>>  > >> Would be happy in efforts and hints to make this run faster.
>>  > >> 
>>  > >> Best regards,
>>  > >> Cartik Sharma
>>  > >> 
>>  > >> 
>>  > >> ___
>>  > >> 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
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>> sender and properly
>>  > >> dispose of the e-mail.
>>  > >> 
>>  > >> 
>>  > >> 
>>  > > 
>>  > 


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Re: [Freesurfer] white matter volume in a ROI

[Douglas N Greve]

For GM area and volume, you can use mris_anatomical_stats. See the 
recent thread on how. For the WM volume, how would you define the WM 
volume that corresponds to you label? We have a routine that parcellates 
WM based on closest proximity to a cortical label.
doug

dolphin...@aol.com wrote:
> Dear FreeSurfer experts,
>
> i have created  a ROI in qdec  , where i have found a significant 
> correlation between lgi and age.
>
> I mapped this ROI to all subjects.
>
> I am interested to compare in this ROI the pial-surface area, the grey 
> matter volume and if possible the white matter volume for this 
> specific region and i am not sure how to do this?
>
> Best regards
>
> Daniel Klein
> 
>
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Re: [Freesurfer] aparc2feat with custom annotation file

[Douglas N Greve]

Yea, this is bug in a program called by aparc2feat. You can get a new 
(Linux version) here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol
doug

Michelle Umali wrote:
> Hi Freesurfers,
> I am trying to generate binary V1 and V2 masks based on my fieldsign 
> results.  We created a custom annotation file by adding the two new 
> areas (muuV1 and muuV2, entries 36 and 37, resp., i.e., in Matlab in 
> rows 37 and 38) to the aparc color table using Matlab and setting all 
> labels to zero. Then we marked the areas in tksurfer (imported the 
> annotation file, made closed paths around the vertices, and added it 
> to the muuV1 or muuV2 label) and exported the annotation file.
>
> This worked fine, but when we used aparc2feat (on feat data previously 
> registered with regfeat2anat) using the --annot  option, 
> only muuV1 (entry 36) was correctly extracted, and there were no 
> entries for label 37 in the resulting volume. 
>
> Do you have any idea what could have gone wrong?
>
> I attached our annotation file (gzipped) containing the marked areas 
> muuV1 and muuV2.
>
> Thank you very much,
> Michelle
>
> 
>
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Re: [Freesurfer] roi analysis from label or annotation

[Douglas N Greve]

It's very hard to tell what you are doing without a command-line. 
Generally, you can pass the full path of a label to surfcluster to make 
it save it in a particular location.
doug

Knut J Bjuland wrote:
> I am working on roi analysis. I have made a label using mri_surdcluster and 
> used mri_label2label to 
> copy the label from fsaverage to each individual subject. The next step would 
> be to use 
> mris_anatomical_stats to calculate stats for each subject. I used a Python to 
> merge the txt file from
> mris_anatomical_stats.
>  
> Is it possible to force mri_surfcluster to save the label another dir than 
> fsaverage? 
> Can I use convert roi label to annotation and then use aparc2stats 
> or similar command to get group statics?
>
>
> Cheers 
> Knut J
> 
>
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Fax: 617-726-7422

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Re: [Freesurfer] mris_anatomical stats different thickness files

[Douglas N Greve]

krista kelly wrote:
> I'm looking at both cortical thickness and surface area differences 
> between two groups. I've been using mris_anatomical_stats to retrieve 
> values but had a few questions:
>
> 1) Do I need to do separate mris_anatomical_stats using different 
> thickness files (bolded below) to get cortical thickness and surface 
> area measures. For example:
>
> cortical thickness - mris_anatomical_stats -l lh.v1.label -t 
> *lh.thickness* -b -f BV01/stats/lh.v1.stats BV01 lh
> surface area - mris_anatomical_stats -l lh.v1.label -t *lh.area *-b -f 
> BV01/stats/lh.v1.stats BV01 lh
>
>  Or, since the output files include all of these measures, is it fine 
> to just run one of the two?
Just run the first one.
>
> 2) The output files for both analyses run above (with different 
> thickness files) have identical values for everything except for tray 
> matter volume. Using lh.thickness file - grayvol = 8082; using lh.area 
> file - grayvol = 4029. Can anyone clarify why this happens?
It computes the gray matter volume by thickness*area. If you pass it 
"area" as the "thickness", then you are probably getting area*area. 
Though I'm surprised that the "thickness" values are correct.
>
> 3) The default surface area values are for the white matter surface. 
> How do I run mri_anatomical_stats to get the pial surface? I've 
> tried mris_anatomical_stats -l lh.v1.label -t *lh.area.pial *-b -f 
> BV01/stats/lh.v1.stats BV01 lh but I get identical values for 
> everything (except grayvol).
Try adding "pial" to the end of the command line (and use lh.thickness)
doug
>
> Thanks!
> Krista
> 
>
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Fax: 617-726-7422

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Re: [Freesurfer] implementation on Neurodebian

[Bruce Fischl]

not yet, although it is something we are working on.

cheers
Bruce
On Mon, 24 Oct 2011, 
Cartik Sharma wrote:



Hi Knut,
Good to know we can speed things up with CUDA. I have a multicore CPU and was 
wondering if
there is a parallelized version of Freesurfer on the CPU.

Thanks for the speedup!

Best regards,
Cartik



On Oct 24, 2011, at 4:41 AM, Knut J Bjuland wrote:

  Hi Cartik

  You use -use-gpu to offload rendering to the GPU using cuda. 

  Knut J

  > From: cartik.sha...@childmind.org
  > To: knut...@hotmail.com
  > Subject: Re: [Freesurfer] implementation on Neurodebian
  > Date: Thu, 20 Oct 2011 15:48:10 +
  > 
  > Hi Knut:
  > 
  > Cool..is this speeding up things by rendering on the GPU.
  > Is there a way to offload computation to the GPU.
  > 
  > Best regards,
  > Cartik
  > 
  > On Oct 20, 2011, at 10:57 AM, Knut J Bjuland wrote:
  > 
  > > Hi Cartik
  > > 
  > > If you enable cuda with -use-gpu the recon-all will run faster.
  > > 
  > > Knut J
  > > 
  > > Den 17.10.2011 16:41, skrev Cartik Sharma:
  > >> Dear Freesurfer developer(s),
  > >> 
  > >> Is there a way to get Freesurfer run faster on Neurodebian. While 
the package produces
  > >> some truly out of the world segmentations and labels for the 
cortical surface, it seems
  > >> to take time.
  > >> 
  > >> For eg:
  > >> Defect correction and retesellation takes an hour, other steps take 
longer..I'm not sure if
  > >> it's the original dataset, the OS platform (i.e Virtual Machine, 
Neurodebian) or original
  > >> computational engine itself.
  > >> 
  > >> Would be happy in efforts and hints to make this run faster.
  > >> 
  > >> Best regards,
  > >> Cartik Sharma
  > >> 
  > >> 
  > >> ___
  > >> Freesurfer mailing list
  > >> Freesurfer@nmr.mgh.harvard.edu
  > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  > >> 
  > >> 
  > >> The information in this e-mail is intended only for the person to 
whom it is
  > >> addressed. If you believe this e-mail was sent to you in error and 
the e-mail
  > >> contains patient information, please contact the Partners Compliance 
HelpLine at
  > >> http://www.partners.org/complianceline . If the e-mail was sent to 
you in error
  > >> but does not contain patient information, please contact the sender 
and properly
  > >> dispose of the e-mail.
  > >> 
  > >> 
  > >> 
  > > 
  > 



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Re: [Freesurfer] matlab script to convert array back to thickness file format?

[Douglas N Greve]

Hi Lara,

I would recommend using
v = MRIread('fname.mgh');
mat = fast_vol2mat(v.vol); % converts any input "volume" to an Ntime 
-by- Nvertices matrix
% perform operations on mat
v2 = v;
v2.vol = fast_mat2vol(mat,v2.volsize);
MRIwrite('fname2.mgh')

The "fast" commands are in $FREESURFER_HOME/fsfast/toolbox.

The structure read in by MRIread has a "vol" field, but this will hold 
any type of pixel data (eg, data on the surface).

doug

Lara Foland-Ross wrote:
> Hi there,
>
> We're using load_mgh.m to load several individual (single subject) cortical 
> thickness maps (each 1X163842) that we'll use to compute a group-level 
> statistic in matlab. We're not changing the dimensionality or order of the 
> information loaded and we would like to know if there is a matlab script we 
> might use to convert our resulting (1X163842) array of statistical values 
> back into a .mgh file that can be read on FreeSurfer. Thanks!
>
> Lara
>
>   

-- 
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MGH-NMR Center
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Fax: 617-726-7422

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Re: [Freesurfer] implementation on Neurodebian

[Cartik Sharma]

Hi Knut,

Good to know we can speed things up with CUDA. I have a multicore CPU and was 
wondering if
there is a parallelized version of Freesurfer on the CPU.

Thanks for the speedup!

Best regards,
Cartik



On Oct 24, 2011, at 4:41 AM, Knut J Bjuland wrote:

Hi Cartik

You use -use-gpu to offload rendering to the GPU using cuda.

Knut J

> From: cartik.sha...@childmind.org
> To: knut...@hotmail.com
> Subject: Re: [Freesurfer] implementation on Neurodebian
> Date: Thu, 20 Oct 2011 15:48:10 +
>
> Hi Knut:
>
> Cool..is this speeding up things by rendering on the GPU.
> Is there a way to offload computation to the GPU.
>
> Best regards,
> Cartik
>
> On Oct 20, 2011, at 10:57 AM, Knut J Bjuland wrote:
>
> > Hi Cartik
> >
> > If you enable cuda with -use-gpu the recon-all will run faster.
> >
> > Knut J
> >
> > Den 17.10.2011 16:41, skrev Cartik Sharma:
> >> Dear Freesurfer developer(s),
> >>
> >> Is there a way to get Freesurfer run faster on Neurodebian. While the 
> >> package produces
> >> some truly out of the world segmentations and labels for the cortical 
> >> surface, it seems
> >> to take time.
> >>
> >> For eg:
> >> Defect correction and retesellation takes an hour, other steps take 
> >> longer..I'm not sure if
> >> it's the original dataset, the OS platform (i.e Virtual Machine, 
> >> Neurodebian) or original
> >> computational engine itself.
> >>
> >> Would be happy in efforts and hints to make this run faster.
> >>
> >> Best regards,
> >> Cartik Sharma
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> The information in this e-mail is intended only for the person to whom it 
> >> is
> >> addressed. If you believe this e-mail was sent to you in error and the 
> >> e-mail
> >> contains patient information, please contact the Partners Compliance 
> >> HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> >> error
> >> but does not contain patient information, please contact the sender and 
> >> properly
> >> dispose of the e-mail.
> >>
> >>
> >>
> >
>

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Re: [Freesurfer] cortical surface of individual subject: coordinates in individual's MNI space

[Douglas N Greve]

For #1, it might be easier to use mri_surf2surf with the --sval-tal-xyz 
option. See the --help for more info.
doug

Bruce Fischl wrote:
> 1. Yes, just apply the talairach.xfm transform to each vertex. Should be 
> easy enough to do in matlab using read_surf.m.
>
> 2. Yes, this can also be done in matlab, saving either in "curv" 
> (write_curv.m) or wfile format.
>
> On Sat, 22 Oct 2011, Nela Cicmil wrote:
>
>   
>> Dear Freesurfer Developers and Users,
>>
>> I have two question(s) about Freesurfer and individual subject's MNI 
>> coordinates:
>>
>> (1) Having run recon-all to reconstruct the cortical surface for an 
>> individual subject in my study, is it possible to obtain the list of 
>> coordinates that describe the points in the individual subject's MNI space 
>> that comprise the cortical surface of that subject's brain? This is in order 
>> to run an MEG beamformer analysis (in matlab) in the subject's own MNI 
>> space, but restricted to those voxels that comprise the cortical surface for 
>> that subject, as calculated by Freesurfer.
>>
>> (2) Once I have obtained (in matlab), for a list of voxels that comprise 
>> 
> the cortical surface, each of the their MNI coordinates and their 
> associated activation value (e.g. tstat), is there a straightforward way to 
> display this on the cortical surface of that subject in tksurfer, for 
> example by converting to a simple wfile?
>   
>> I searched the archives but could not find information that explained 
>> 
> this directly; apologies if this does already exist: if so, could you 
> please point me towards it?
>   
>> Thank you so much for your help,
>>
>> Best wishes,
>> Nela
>>
>>
>> 
>> Nela Cicmil
>> D.Phil Candidate, Neurophysiology
>> Dept. Physiology, Anatomy & Genetics
>> University of Oxford
>>
>> Tel: 01865 282274
>> Internal: 82274
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>>
>>
>> 
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>
>   

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[Freesurfer] white matter volume in a ROI

[dolphinede]

Dear FreeSurfer experts,

i have created  a ROI in qdec  , where i have found a significant correlation 
between lgi and age.

I mapped this ROI to all subjects. 

I am interested to compare in this ROI the pial-surface area, the grey matter 
volume and if possible the white matter volume for this specific region and i 
am not sure how to do this?

Best regards 

Daniel Klein
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