Re: [Freesurfer] Error in dt_recon

[Ramesh Babu]

External Email - Use Caution

Dear Douglas,
Thank you so much. It's done.
Regards
Ramesh

On Tue, Sep 17, 2024, 7:34 PM Douglas N. Greve 
wrote:

> The argument to the --s flag should be the name of the subject as was
> specified when you ran recon-all, eg
> recon-all -i t1_SPGR.nii  -s subjectname -all
> Then use dt_rcon -s subjectname ...
>
> On 9/12/2024 7:45 AM, Ramesh Babu wrote:
>
> External Email - Use Caution
> Dear All,
>
> I am new to dti analysis. I am trying analysis in a single subject. I set
> the environment as mentioned below.
> export DTI_DATA=export
> DTI_DATA=/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis
> export SUBJECTS_DIR=$DTI_DATA/subjects/t1_data/
>
> In the last step, I received this error.
> dt_recon --i dti_data.nii --b bvals.txt bvecs.txt --s
> $SUBJECTS_DIR/t1_SPGR.nii --o dtioutput2
> error:
> mghRead(/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis/subjects/t1_data//t1_SPGR.nii/mri/brainmask.mgz,
> -1): could not open file
>
> How to get this brain mask? Should it be from subject T1 image or bo map?
> I attached the full error report as a text file.
> I kindly request you to provide me with a solution.
>
> Thanks in advance
> Ramesh
>
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[Freesurfer] Error in dt_recon

[Ramesh Babu]

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Dear All,

I am new to dti analysis. I am trying analysis in a single subject. I set
the environment as mentioned below.
export DTI_DATA=export
DTI_DATA=/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis
export SUBJECTS_DIR=$DTI_DATA/subjects/t1_data/

In the last step, I received this error.
dt_recon --i dti_data.nii --b bvals.txt bvecs.txt --s
$SUBJECTS_DIR/t1_SPGR.nii --o dtioutput2
error:
mghRead(/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis/subjects/t1_data//t1_SPGR.nii/mri/brainmask.mgz,
-1): could not open file

How to get this brain mask? Should it be from subject T1 image or bo map?
I attached the full error report as a text file.
I kindly request you to provide me with a solution.

Thanks in advance
Ramesh


dt_recon
Description: Binary data
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[Freesurfer] Freeview issue

[Ramesh Babu]

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Dear Expert,
Recently I installed the latest version of freesurfer in Ubuntu OS 22LTS..
Freesurfer is installed successfully, but freeview gives some errors which
I pasted below. Please provide your suggestions.

Thank You
Ramesh

freeview
This application failed to start because no Qt platform plugin could be
initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl,
offscreen, vnc, wayland-egl, wayland, webgl, xcb.

Aborted (core dumped)
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[Freesurfer] Freesurfer installation issue

[Ramesh Babu]

External Email - Use Caution

Dear Expert,

I am trying to install Freesurfer-7.2 .deb package. I had this package
earlier, and after formatting my system now, I am trying to install
Freesurfer again. But I am facing the following issues.

'freesurfer_7.2.0_amd64.deb' is not a Debian format archive
dpkg: error processing archive freesurfer_7.2.0_amd64.deb (--install):
 dpkg-deb --control subprocess returned error exit status 2
Errors were encountered while processing:
 freesurfer_7.2.0_amd64.deb

Kindly request you to provide a solution to solve this issue.

Thanks in advance
Ramesh
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Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

[Ramesh Babu]

External Email - Use Caution

Dear Douglas

Thank you very much for your suggestions.

Regards
Ramesh

On Tue, 6 Apr, 2021, 7:03 PM Douglas N. Greve, 
wrote:

> Twice the same image at 1x1x1, then use mri_robust_template to register
> and average them together
>
> On 4/6/2021 8:10 AM, Ramesh Babu wrote:
>
> External Email - Use Caution
> Dear Eugenio and Philipp,
>
> Thank you very much for your suggestions. Could you please give more input
> on "acquire the T1WI double and average it after coregistration, this
> increases the SNR".
>
> Should aquire twise the same sequence with 1x1x2 voxel dimension?
>
> Thanks
> Ramesh
>
>
> On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E., <
> jiglesiasgonza...@mgh.harvard.edu> wrote:
>
>> That all sounds right, thanks a lot Philipp!
>>
>>
>>
>>
>>
>> Juan Eugenio Iglesias
>>
>> Senior research fellow
>>
>> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>>
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be* 
>> http://secure-web.cisco.com/1oAFYauOAeFEI_KJ-fkusgflgO_3xjRHgp7o7CJ3qp41OmNYAHMlvp6Zy_mjFrQna2xraD05zLX72T9k2ZNBxJHPp1lNSv83SmEbFU-GoXpEbCDc6Q36FWCkmfvBgltRRW_zqFZ58dkXw9EZSUQecxsHx9d2bRyl43Zs-sEfD1usXImJGYxchdZJAIb7dU6dJ-hMgC4PeXJDUIO_QfEwqT5pH-JkIZcHhI6CiPacx2HMtkfH3Uq49XZ3cLxtL4H89WL1NSermiy9IwrlG1XBASQ/http%3A%2F%2Fwww.jeiglesias.com
>> <http://secure-web.cisco.com/1yAlNRge1To1jCEouu9JnBYJFnIJRo-86GCJ4EIWmAyj8pkkdBifGwyirgDc1KI-N6H7_dg4rBnLgE3CaKBeQuxL7GotNy9SzxKSD4OusIQrdGgcD_E0ObeWLPWYbYhFPgBDLEjcGPr-D8PT-k8bLD71quTve1q2fA_-MJY73fb-zPWX2QNDMT39_ceuRLWK8XGl18IGjSIXm6QeDK2erHCdQTO-rww0uRlSIph9mtjeVoEggFnM0sluSy0XceT-MPg9TJwCFg8RuNNq4J20pSw/http%3A%2F%2Fwww.jeiglesias.com>
>>
>>
>>
>>
>>
>>
>>
>>
>> *From: * on behalf of "Saemann,
>> Philipp" 
>> *Reply-To: *Freesurfer support list 
>> *Date: *Friday, April 2, 2021 at 03:51
>> *To: *Freesurfer support list , Umesh
>> Rurdrapatna 
>> *Subject: *Re: [Freesurfer] 2mm thick image for hippocampal segmentation.
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi,
>>
>>
>>
>> I try to answer but Eugenio may also add comments. Several points that
>> are important:
>>
>> - 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can
>> manage.
>>
>> - Post-aquisition reslicing to a higher resolution does not really
>> increase the information content. Internally the algorithm works at a much
>> higher resolution, anyway.
>>
>> - If possible, switch to 3 Tesla.
>>
>> - If possible and this is a prospective study, add a coronal T2 image and
>> use the bi-channel option. See papers of Iglesias et al. on this.
>>
>> - What you could also do on a 1.5 T is acquire the T1WI double and
>> average it after coregistration, this increases the SNR.
>>
>> - Generally, isometric resolutions are good due to the symmetry, of
>> course.
>>
>> - Also on 1.5 T, you may go bit below 1 mm with good head immobilization,
>> and a longer scanning time. BRAVO in general is a good T1 option.
>>
>>
>>
>> Best,
>>
>> Philipp
>>
>>
>> --
>>
>> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Ramesh Babu <
>> mgrameshbabu2...@gmail.com>
>> *Gesendet:* Freitag, 2. April 2021 09:29
>> *An:* Freesurfer support list; Umesh Rurdrapatna
>> *Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal segmentation.
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Dear experts,
>>
>> Sorry for reposting. I am expecting some response from experts, so that I
>> can proceed with confidence.
>>
>> For our project work, we are looking for hippocampal  and its
>> subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with
>> 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced
>> images with a lot of noise. Then we tried the same sequence with 1x1x2
>> resolution, and 256x256x80 FOV, which produced a clean image without noise.
>> When we reformatted the images, it produces 0.5x0.5x1 resolution with
>> 512x512x172 dimension.
>>
>>
>>
>> Is this sequence good for hippocampal volume estimation and subfield
>> segmentation (also for whole-brain VBM analysis)?
>>
>> Could yo

Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

[Ramesh Babu]

External Email - Use Caution

Dear Eugenio and Philipp,

Thank you very much for your suggestions. Could you please give more input
on "acquire the T1WI double and average it after coregistration, this
increases the SNR".

Should aquire twise the same sequence with 1x1x2 voxel dimension?

Thanks
Ramesh


On Fri, 2 Apr, 2021, 9:00 PM Iglesias Gonzalez, Juan E., <
jiglesiasgonza...@mgh.harvard.edu> wrote:

> That all sounds right, thanks a lot Philipp!
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://secure-web.cisco.com/1yAlNRge1To1jCEouu9JnBYJFnIJRo-86GCJ4EIWmAyj8pkkdBifGwyirgDc1KI-N6H7_dg4rBnLgE3CaKBeQuxL7GotNy9SzxKSD4OusIQrdGgcD_E0ObeWLPWYbYhFPgBDLEjcGPr-D8PT-k8bLD71quTve1q2fA_-MJY73fb-zPWX2QNDMT39_ceuRLWK8XGl18IGjSIXm6QeDK2erHCdQTO-rww0uRlSIph9mtjeVoEggFnM0sluSy0XceT-MPg9TJwCFg8RuNNq4J20pSw/http%3A%2F%2Fwww.jeiglesias.com
>
>
>
>
>
>
>
> *From: * on behalf of "Saemann,
> Philipp" 
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, April 2, 2021 at 03:51
> *To: *Freesurfer support list , Umesh
> Rurdrapatna 
> *Subject: *Re: [Freesurfer] 2mm thick image for hippocampal segmentation.
>
>
>
> *External Email - Use Caution*
>
> Hi,
>
>
>
> I try to answer but Eugenio may also add comments. Several points that are
> important:
>
> - 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can
> manage.
>
> - Post-aquisition reslicing to a higher resolution does not really
> increase the information content. Internally the algorithm works at a much
> higher resolution, anyway.
>
> - If possible, switch to 3 Tesla.
>
> - If possible and this is a prospective study, add a coronal T2 image and
> use the bi-channel option. See papers of Iglesias et al. on this.
>
> - What you could also do on a 1.5 T is acquire the T1WI double and average
> it after coregistration, this increases the SNR.
>
> - Generally, isometric resolutions are good due to the symmetry, of course.
>
> - Also on 1.5 T, you may go bit below 1 mm with good head immobilization,
> and a longer scanning time. BRAVO in general is a good T1 option.
>
>
>
> Best,
>
> Philipp
>
>
> --
>
> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Ramesh Babu <
> mgrameshbabu2...@gmail.com>
> *Gesendet:* Freitag, 2. April 2021 09:29
> *An:* Freesurfer support list; Umesh Rurdrapatna
> *Betreff:* Re: [Freesurfer] 2mm thick image for hippocampal segmentation.
>
>
>
> *External Email - Use Caution*
>
> Dear experts,
>
> Sorry for reposting. I am expecting some response from experts, so that I
> can proceed with confidence.
>
> For our project work, we are looking for hippocampal  and its
> subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with
> 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced
> images with a lot of noise. Then we tried the same sequence with 1x1x2
> resolution, and 256x256x80 FOV, which produced a clean image without noise.
> When we reformatted the images, it produces 0.5x0.5x1 resolution with
> 512x512x172 dimension.
>
>
>
> Is this sequence good for hippocampal volume estimation and subfield
> segmentation (also for whole-brain VBM analysis)?
>
> Could you please suggest to me a correct sequence, if need to be changed?
>
>
>
> Regards
>
> Ramesh
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Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

[Ramesh Babu]

External Email - Use Caution

Dear experts,
Sorry for reposting. I am expecting some response from experts, so that I
can proceed with confidence.
For our project work, we are looking for hippocampal  and its
subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with
1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced
images with a lot of noise. Then we tried the same sequence with 1x1x2
resolution, and 256x256x80 FOV, which produced a clean image without noise.
When we reformatted the images, it produces 0.5x0.5x1 resolution with
512x512x172 dimension.

Is this sequence good for hippocampal volume estimation and subfield
segmentation (also for whole-brain VBM analysis)?
Could you please suggest to me a correct sequence, if need to be changed?

Regards
Ramesh
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[Freesurfer] 2mm thick image for hippocampal segmentation.

[Ramesh Babu]

External Email - Use Caution

Dear Experts,

For our project work, we particularly looking for hippocampal and its
subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with
1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced
images with a lot of noise. Then we tried the same sequence with 1x1x2
resolution, and 256x256x80 FOV, which produced a clean image without noise.
When we reformatted the images, it produces 0.5x0.5x1 resolution with
512x512x172 dimension.

Is this sequence good for hippocampal volume estimation and subfield
segmentation (also for whole-brain VBM analysis)?
Could you please suggest to me a correct sequence for our project?

Regards
Ramesh
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[Freesurfer] Flip image (resize)

[Ramesh Babu]

External Email - Use Caution

Dear Experts,

The fMRI data, when viewed in SPM, some images have 3x3x4 voxel dimensions
and some images have -3x3x4. Should I flip the image (using resize option)
so that all images will have the same dimensions? or Should I leave it
without flipping?

Please give your suggestions.

Regards
Ramesh
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Re: [Freesurfer] Using subject specific template, atlas, & TPM

[Ramesh Babu]

Dear Bruce and Douglas,

Thank you for your suggestions. I am trying it and will need your
suggestions on result.

Thank you
Ramesh

On Fri, Jan 19, 2018 at 2:08 AM, Douglas Greve 
wrote:

> you can use gcatrain (and jkgcatrain for testing) if you are using v6
>
> On 1/12/18 3:27 PM, Bruce Fischl wrote:
>
> Hi Ramesh
>
> if you have segmentations in our aseg format (or edited asegs for that
> matter if you find them not accurate enough), you should be able to use
> mri_ca_train to genenerate a new .gca file and apply it to your subjects.
> Read the help and wiki and see if you can make it work, and let us knof i
> you have any issues. There are also surface-based atlases, but I suspect
> thos are a lot less likely to be biased by brain shape (since we map to a
> sphere anyway)
>
> cheers
> Bruce
> On Fri, 12 Jan 2018, Ramesh Babu wrote:
>
> Dear Bruce,
> Thank you for your prompt response. I have 2 groups & 40 subjects in each
> groups in my study. I am
> using freesurfer and various other software for analysis. I found that the
> template available for
> registration either western or Chinese. There is no template available for
> Indian brain population.
> Therefore we want to develop a template specific to our population. And we
> have created templates
> using different software and want to compare the result with default
> template (western brain
> template) and our template. I need your help how to use this template in
> freesurfer. As you
> mentioned in the previous mail I will try with training utility
> (mri_ca_train). Can I get any user
> guide to know details about it?
>
> Thank you
> Ramesh
>
> On Thu, Jan 11, 2018 at 11:07 PM, Bruce Fischl
>   wrote:
>   Hi Ramesh
>
>   what are you trying to achieve? Our segmentation tools use their own
> format as they need
>   information not contained in most standard images, so it won't be
> easy to get it into
>   that format unless you use our training utility (mri_ca_train)
>
>   cheers
>   Bruce
>   On Thu, 11 Jan 2018, Ramesh Babu wrote:
>
> Dear experts,
> I have analysed T1 data using Freesurfer. Now we have created
> atlas,
> template & tissue probability
> map using different methods and softwares. I need your help to
> use template
> in freesufer, so that we
> can compare with default template and our template. Please
> help me to put
> these images in
> appropriate folders in Freesurfer.
>
>
> Thank you
> RB
>
>
>
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> dispose of the e-mail.
>
>
>
>
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Re: [Freesurfer] Using subject specific template, atlas, & TPM

[Ramesh Babu]

Dear Bruce,

Thank you for your prompt response. I have 2 groups & 40 subjects in each
groups in my study. I am using freesurfer and various other software for
analysis. I found that the template available for registration either
western or Chinese. There is no template available for Indian brain
population. Therefore we want to develop a template specific to our
population. And we have created templates using different software and want
to compare the result with default template (western brain template) and
our template. I need your help how to use this template in freesurfer. As
you mentioned in the previous mail I will try with training utility
(mri_ca_train).
Can I get any user guide to know details about it?

Thank you
Ramesh

On Thu, Jan 11, 2018 at 11:07 PM, Bruce Fischl 
wrote:

> Hi Ramesh
>
> what are you trying to achieve? Our segmentation tools use their own
> format as they need information not contained in most standard images, so
> it won't be easy to get it into that format unless you use our training
> utility (mri_ca_train)
>
> cheers
> Bruce
>
> On Thu, 11 Jan 2018, Ramesh Babu wrote:
>
> Dear experts,
>> I have analysed T1 data using Freesurfer. Now we have created atlas,
>> template & tissue probability
>> map using different methods and softwares. I need your help to use
>> template in freesufer, so that we
>> can compare with default template and our template. Please help me to put
>> these images in
>> appropriate folders in Freesurfer.
>>
>>
>> Thank you
>> RB
>>
>>
>>
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[Freesurfer] Using subject specific template, atlas, & TPM

[Ramesh Babu]

Dear experts,

I have analysed T1 data using Freesurfer. Now we have created atlas,
template & tissue probability map using different methods and softwares. I
need your help to use template in freesufer, so that we can compare with
default template and our template. Please help me to put these images in
appropriate folders in Freesurfer.


Thank you
RB
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Re: [Freesurfer] non-brain region

[Ramesh Babu]

Dear Emma,

Thank you for your opinion,

Ramesh

On Thu, Dec 7, 2017 at 9:54 PM, Boyd, Emma  wrote:

> Hi Ramesh,
>
>
> Unless these non-brain regions affect the surfaces then it is fine to
> leave it as is. Your image looks fine to me.
>
>
> Emma
>
>
>
> -
>
> Emma Boyd
>
> Research Technician II
>
> Laboratory for Computational Neuroimaging
>
> Martinos Center for Biomedical Imaging
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ramesh Babu <
> mgrameshbabu2...@gmail.com>
> *Sent:* Thursday, December 7, 2017 6:49 AM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] non-brain region
>
> Dear Experts,
>
> I performed recon-all all precess and it finished without any error.
> However I found some parts of non-brain regions are left over. Should I
> correct it or I can leave it? Please see the attached file and give your
> suggestions.
>
> Thanks in advance
> RB
>
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Re: [Freesurfer] Merging two groups

[Ramesh Babu]

Dear Bruce,

Thank you. Now its working fine.

On Thu, Nov 30, 2017 at 3:46 PM, Ramesh Babu 
wrote:

> Dear Bruce,
> Thank you very much for reply.
>
> I have to link fsavarage also. Because recently I have formated my system,
> the link between freesurfer and fsaverage is broken.
> I hope following link will be the correct one. If not please correct me.
>
> ln -s /usr/local/freesurfer/subjects/fsaverage
> /mnt/backup_data/freesurfer_analysis/subjects/fsaverage
>
> On Wed, Nov 29, 2017 at 8:38 PM, Bruce Fischl 
> wrote:
>
>> if you have two dirs, dir1 and dir2, with a set of subjects in each
>> (subjects1 and subjects2), you would do:
>>
>> cd $dir2
>> foreach s ($subjects1)
>>   ln -s $dir1/$s
>> end
>>
>> then all your subjects will be listed in dir2
>>
>> that should do the trick
>>
>> On Wed, 29 Nov 2017, Ramesh Babu wrote:
>>
>> Dear Bruce,
>>>
>>> Thank for your reply. I am getting confusion in creating symlink.
>>> ln -s /usr/local/freesurfer/subjects/fsaverage
>>> /mnt/backup_data/freesurfer_analysis/subjects/
>>> ln -s /usr/local/freesurfer/subjects/fsaverage
>>> /mnt/backup_data/freesurfer_analysis/subjects/fsaverage
>>>
>>>
>>> Please let me know how to create symbolic link?
>>>
>>> Thank you
>>> Ramesh
>>>
>>> On Tue, Nov 28, 2017 at 8:27 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>>   Hi Ramesh
>>>
>>>   probably easiest to symlink them
>>>
>>>   cheers
>>>   Bruce
>>>   On Tue, 28 Nov 2017, Ramesh Babu wrote:
>>>
>>> Hi, I have done recon-all -all processing for 2 groups in
>>> separate subjects directories. I want to
>>> put all subjects in one dkirectory. Should I copy paste all
>>> subject’s folders in one directory or
>>> is
>>> there any others steps to merge?
>>>
>>> Thanks in advance
>>> RB
>>>
>>>
>>>
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>>> HelpLine at
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>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
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Re: [Freesurfer] Merging two groups

[Ramesh Babu]

Dear Bruce,
Thank you very much for reply.

I have to link fsavarage also. Because recently I have formated my system,
the link between freesurfer and fsaverage is broken.
I hope following link will be the correct one. If not please correct me.

ln -s /usr/local/freesurfer/subjects/fsaverage
/mnt/backup_data/freesurfer_analysis/subjects/fsaverage

On Wed, Nov 29, 2017 at 8:38 PM, Bruce Fischl 
wrote:

> if you have two dirs, dir1 and dir2, with a set of subjects in each
> (subjects1 and subjects2), you would do:
>
> cd $dir2
> foreach s ($subjects1)
>   ln -s $dir1/$s
> end
>
> then all your subjects will be listed in dir2
>
> that should do the trick
>
> On Wed, 29 Nov 2017, Ramesh Babu wrote:
>
> Dear Bruce,
>>
>> Thank for your reply. I am getting confusion in creating symlink.
>> ln -s /usr/local/freesurfer/subjects/fsaverage
>> /mnt/backup_data/freesurfer_analysis/subjects/
>> ln -s /usr/local/freesurfer/subjects/fsaverage
>> /mnt/backup_data/freesurfer_analysis/subjects/fsaverage
>>
>>
>> Please let me know how to create symbolic link?
>>
>> Thank you
>> Ramesh
>>
>> On Tue, Nov 28, 2017 at 8:27 PM, Bruce Fischl 
>> wrote:
>>   Hi Ramesh
>>
>>   probably easiest to symlink them
>>
>>   cheers
>>   Bruce
>>   On Tue, 28 Nov 2017, Ramesh Babu wrote:
>>
>> Hi, I have done recon-all -all processing for 2 groups in
>> separate subjects directories. I want to
>> put all subjects in one dkirectory. Should I copy paste all
>> subject’s folders in one directory or
>> is
>> there any others steps to merge?
>>
>> Thanks in advance
>> RB
>>
>>
>>
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>> but does not contain patient information, please contact the sender and
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>>
>>
>>
>>
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Re: [Freesurfer] Merging two groups

[Ramesh Babu]

Dear Bruce,

Thank for your reply. I am getting confusion in creating symlink.
ln -s /usr/local/freesurfer/subjects/fsaverage
/mnt/backup_data/freesurfer_analysis/subjects/
ln -s /usr/local/freesurfer/subjects/fsaverage
/mnt/backup_data/freesurfer_analysis/subjects/fsaverage


Please let me know how to create symbolic link?

Thank you
Ramesh

On Tue, Nov 28, 2017 at 8:27 PM, Bruce Fischl 
wrote:

> Hi Ramesh
>
> probably easiest to symlink them
>
> cheers
> Bruce
>
> On Tue, 28 Nov 2017, Ramesh Babu wrote:
>
> Hi, I have done recon-all -all processing for 2 groups in separate
>> subjects directories. I want to
>> put all subjects in one dkirectory. Should I copy paste all
>> subject’s folders in one directory or is
>> there any others steps to merge?
>>
>> Thanks in advance
>> RB
>>
>>
>>
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Re: [Freesurfer] Merging two groups

[Ramesh Babu]

Thank you very much for your reply.

On Mon, Nov 27, 2017 at 10:51 PM, Douglas N Greve  wrote:

> An easy solution is just to use a symbolic link (the ln command under
> linux). That way you don't have to move anything at all. If you want to
> move things, I would copy them, make sure the copy is ok, then delete
> the old version. rsync is good for this kind of thing too
>
>
> On 11/27/2017 12:14 PM, Ramesh Babu wrote:
> > Hi,
> > I have done recon-all -all processing for 2 groups in separate
> > subjects directories. I want to put all subjects in one dkirectory.
> > Should I copy paste all subject’s folders in one directory or is there
> > any others steps to merge?
> >
> > Thanks in advance
> > RB
> >
> >
> >
> > ___
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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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> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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[Freesurfer] Merging two groups

[Ramesh Babu]

Hi,
I have done recon-all -all processing for 2 groups in separate subjects
directories. I want to put all subjects in one dkirectory. Should I copy
paste all subject’s folders in one directory or is there any others steps
to merge?

Thanks in advance
RB
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[Freesurfer] Merging two groups

[Ramesh Babu]

Hi,
I have done recon-all -all processing for 2 groups in separate subjects
directories. I want to put all subjects in one dkirectory. Should I copy
paste all subject’s folders in one directory or is there any others steps
to merge?

Thanks in advance
RB
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Re: [Freesurfer] Changing operating system.

[Ramesh Babu]

Thank you very much for your suggestions
RB

On Saturday, November 11, 2017, Bruce Fischl 
wrote:

> some of this is dependent on things out of our control (e.g. third party
> libraries and such). Certainly rerunning is the safest thing to do, but if
> that is too much of a burden you could rerun a couple and see if things
> change.
>
> cheers
> Bruce
>
>
> On Sat, 11 Nov 2017, Ramesh Babu wrote:
>
> Dear Experts,
>>
>> Recently I am facing lot of problem with Ubuntu OS 16lts. In one year I
>> have formatted 4 times
>> because of nvidia graphic card driver issue (happens after update) or
>> some unknown reason ( I am not
>> tech tech guy to figure out all the problem). Yesterday onwards problem
>> started again. I couldn't
>> open ubuntu. Initially it was blank screen, after following some
>> suggestion from forum I removed
>> nvidia driver and tried lot other things. Still not functioning.
>> Therefore I am planning to go for
>> cent os.
>>
>> After installing cent os should I redo all analysis again? or I can
>> continue with whatever so far
>> done by using Ubuntu os?
>>
>> Thanks
>> RB
>>
>>
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[Freesurfer] Changing operating system.

[Ramesh Babu]

Dear Experts,

Recently I am facing lot of problem with Ubuntu OS 16lts. In one year I
have formatted 4 times because of nvidia graphic card driver issue (happens
after update) or some unknown reason ( I am not tech tech guy to figure out
all the problem). Yesterday onwards problem started again. I couldn't open
ubuntu. Initially it was blank screen, after following some suggestion from
forum I removed nvidia driver and tried lot other things. Still not
functioning. Therefore I am planning to go for cent os.

After installing cent os should I redo all analysis again? or I can
continue with whatever so far done by using Ubuntu os?

Thanks
RB
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[Freesurfer] Selecting OS for image analysis

[Ramesh Babu]

Dear Experts,
I have purchased a new pc. I want to use for MRI and EEG analysis by using
MATLAB, FSL, SPM, Fresurfer etc,. Which OS is suitable to handle these
software?
I have NVIDIA graphics card 610 in my system.

I am using Ubuntu in another systm and little bit of experience in cent os.


Thank in advance
Ramesh
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Re: [Freesurfer] error report - talairach.m3z not found

[Ramesh Babu]

Thank you Bruce

On Thu, Jun 22, 2017 at 12:45 AM, Bruce Fischl 
wrote:

> sounds like more in the graphics  card, or just reduce the number of
> simultaneous jobs
>
> On Wed, 21 Jun 2017, Ramesh Babu wrote:
>
> Dear Douglas Greve and Bruce,
>>
>> Thanks for your reply. I am using 16GB RAM and 2 GB graphic card. Should
>> I increase memory of both or only graphic card?
>>
>> Thanks
>> Ramesh
>>
>> On Tue, Jun 20, 2017 at 9:02 PM, Bruce Fischl 
>> wrote:
>>   or don't run so many at the same time
>>
>>   cheers
>>   Bruce
>>   On Tue, 20 Jun 2017, Douglas Greve
>>   wrote:
>>
>>   >
>>   > The error was earlier:
>>   >
>>   > CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of
>> memory.
>>   > Abort (core dumped)
>>   > ERROR: mri_ca_register with non-zero status 134
>>   >
>>   > looks like you need more memory in your gpu
>>   >
>>   > On 6/20/17 7:30 AM, Ramesh Babu wrote:
>>   >   Dear Expert,
>>   >
>>   > The recon-all -all process has stopped abruptly and error report
>> shows
>>   > that "cannot find or read transforms/talairach.m3z". Please see
>> the
>>   > attached file. Processing was running in 5 terminal
>> simultaneously and
>>   > it has happened for two processing. Others exited without error.
>> Could
>>   > please tell what should I do to continue the interrupted one.
>>   >
>>   > Thanks in advance
>>   > Ramesh
>>   >
>>   >
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> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
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Re: [Freesurfer] error report - talairach.m3z not found

[Ramesh Babu]

Dear Douglas Greve and Bruce,

Thanks for your reply. I am using 16GB RAM and 2 GB graphic card. Should I
increase memory of both or only graphic card?

Thanks
Ramesh

On Tue, Jun 20, 2017 at 9:02 PM, Bruce Fischl 
wrote:

> or don't run so many at the same time
>
> cheers
> Bruce
> On Tue, 20 Jun 2017, Douglas Greve
> wrote:
>
> >
> > The error was earlier:
> >
> > CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory.
> > Abort (core dumped)
> > ERROR: mri_ca_register with non-zero status 134
> >
> > looks like you need more memory in your gpu
> >
> > On 6/20/17 7:30 AM, Ramesh Babu wrote:
> >   Dear Expert,
> >
> > The recon-all -all process has stopped abruptly and error report shows
> > that "cannot find or read transforms/talairach.m3z". Please see the
> > attached file. Processing was running in 5 terminal simultaneously and
> > it has happened for two processing. Others exited without error. Could
> > please tell what should I do to continue the interrupted one.
> >
> > Thanks in advance
> > Ramesh
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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> >
> >
> >
> >
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
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[Freesurfer] error report - talairach.m3z not found

[Ramesh Babu]

Dear Expert,

The recon-all -all process has stopped abruptly and error report shows that
"cannot find or read transforms/talairach.m3z". Please see the attached
file. Processing was running in 5 terminal simultaneously and it has
happened for two processing. Others exited without error. Could please tell
what should I do to continue the interrupted one.

Thanks in advance
Ramesh
Mon Jun 19 21:28:05 IST 2017
/mnt/research/freesurfer_analysis/subjects/grp147
/usr/local/freesurfer/bin/recon-all
-all -i grp147_t1.nii -s grp147 -sd subjects -use-gpu
subjid grp147
setenv SUBJECTS_DIR /mnt/research/freesurfer_analysis/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux rameshbabu 4.4.0-79-generic #100-Ubuntu SMP Wed May 17 19:58:14 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  63592 
maxlocks unlimited
maxsignal63592 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   16326760 1255880 6630512   30092 844036814665140
Swap:  16669692   016669692


program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/19-15:58:05-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-79-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/19-15:58:05-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-79-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/19-15:58:05-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-79-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/19-15:58:05-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-79-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/19-15:58:05-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-79-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/19-15:58:05-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-79-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/19-15:58:05-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-79-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/19-15:58:05-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-79-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/19-15:58:05-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10

Re: [Freesurfer] recon-all -all error end abruptly

[Ramesh Babu]

Dear Bruce,
I  am using 16 GB RAM. Should I increase RAM OR upgrade my graphic card?

Thanks
Ramesh

On Tuesday, June 6, 2017, Bruce Fischl  wrote:

> Hi Ramesh
>
> just the same one as before - you ran out of memory, likely because
> something else was running at the same time
>
> cheers
> Bruce
> On Tue, 6 Jun 2017, Ramesh Babu wrote:
>
> Dear Bruce,
>>
>> Today I ran the image processing on the same image which was stopped
>> abruptly earlier. Now it is finished without any error. Please see the
>> attached file before and after error and give your suggestions.
>>
>> Thanks
>> Ramesh
>>
>> On Mon, Jun 5, 2017 at 8:31 PM, Ramesh Babu 
>> wrote:
>>   Sure. I will start now. Tomorrow I will send the report.
>>
>> Thanks
>> Ramesh
>>
>> On Mon, Jun 5, 2017 at 8:26 PM, Bruce Fischl
>>  wrote:
>>   Hi Ramesh
>>
>>   we don't do any automatic updating. Can you try running
>>   one of them again with nothing else running and see if it
>>   completes?
>>
>>   cheers
>>   Bruce
>>   On Mon, 5 Jun 2017, Ramesh Babu wrote:
>>
>> Dear Bruce,
>>
>> Please see the attached file which was
>> completed normally. Earlier I have
>> done this with 6 images simultaneously without
>> any problem. But yesterday
>> out of 6 image processing two went out of
>> memory and stopped. I feel some
>> automatic update would have happened. I am not
>> sure.
>>
>> What should I do to avoid such problem?
>>
>> Thanks
>> Ramesh
>>
>>
>>
>> On Mon, Jun 5, 2017 at 7:39 PM, Bruce Fischl
>> 
>>     wrote:
>>   Hi Ramesh
>>
>>   the error log has a line where the GPU
>> says it ran out of
>>   memory. Possibly other things were
>> running?
>>   cheers
>>   Bruce
>>   On Mon, 5 Jun 2017, Ramesh Babu wrote:
>>
>> Dear Bruce,
>>
>> Two days back I ran 6 image
>> processing simultaneous
>> in different terminal.
>> Everything finished without any
>> error and took 8.2
>> hrs (4.5 hrs if I use
>> only one terminal). But yesterday
>> this problem has
>> happened for the first
>> time.
>>
>> I am using Intel® Core™ i7-4790
>> CPU @ 3.60GHz × 8
>> processor with 15.6 GiB
>> ram, GeForce GT 610/PCIe/SSE2  2GB
>> graphic card.
>> What should I do to
>> increase my memory?
>>
>> Thanks
>> Ramesh
>>
>> On Mon, Jun 5, 2017 at 7:21 PM,
>> Bruce Fischl
>> 
>> wrote:
>>   it looks like you are trying
>> to run the cuda
>> version but your
>>   GPU doesn't
>>   have enough memory
>>
>>   cheers
>>   Bruce
>>   On Mon, 5 Jun 2017, Ramesh
>> Babu wrote:
>>
>>   > Dear Expert,
>>   >
>>   > recon-all -all process for
>> one subject end
>> abruptly. I have
>>   attached the
>>   > error report file. Please
>> provide me some
>> solution.
>>   >
>>   >
>>   > Thanks
>>   > Ramesh
>>   >
>>   >
>>   >
>>
>> ___
>>

Re: [Freesurfer] recon-all -all error end abruptly

[Ramesh Babu]

Sure. I will start now. Tomorrow I will send the report.

Thanks
Ramesh

On Mon, Jun 5, 2017 at 8:26 PM, Bruce Fischl 
wrote:

> Hi Ramesh
>
> we don't do any automatic updating. Can you try running one of them again
> with nothing else running and see if it completes?
>
>
> cheers
> Bruce
> On Mon, 5 Jun 2017, Ramesh Babu wrote:
>
> Dear Bruce,
>>
>> Please see the attached file which was completed normally. Earlier I have
>> done this with 6 images simultaneously without any problem. But yesterday
>> out of 6 image processing two went out of memory and stopped. I feel some
>> automatic update would have happened. I am not sure.
>>
>> What should I do to avoid such problem?
>>
>> Thanks
>> Ramesh
>>
>>
>>
>> On Mon, Jun 5, 2017 at 7:39 PM, Bruce Fischl 
>> wrote:
>>   Hi Ramesh
>>
>>   the error log has a line where the GPU says it ran out of
>>   memory. Possibly other things were running?
>>   cheers
>>   Bruce
>>   On Mon, 5 Jun 2017, Ramesh Babu wrote:
>>
>> Dear Bruce,
>>
>> Two days back I ran 6 image processing simultaneous
>> in different terminal.
>> Everything finished without any error and took 8.2
>> hrs (4.5 hrs if I use
>> only one terminal). But yesterday this problem has
>> happened for the first
>> time.
>>
>> I am using Intel® Core™ i7-4790 CPU @ 3.60GHz × 8
>> processor with 15.6 GiB
>> ram, GeForce GT 610/PCIe/SSE2  2GB graphic card.
>> What should I do to
>> increase my memory?
>>
>> Thanks
>> Ramesh
>>
>> On Mon, Jun 5, 2017 at 7:21 PM, Bruce Fischl
>>     
>> wrote:
>>   it looks like you are trying to run the cuda
>> version but your
>>   GPU doesn't
>>   have enough memory
>>
>>   cheers
>>   Bruce
>>   On Mon, 5 Jun 2017, Ramesh Babu wrote:
>>
>>   > Dear Expert,
>>   >
>>   > recon-all -all process for one subject end
>> abruptly. I have
>>   attached the
>>   > error report file. Please provide me some
>> solution.
>>   >
>>   >
>>   > Thanks
>>   > Ramesh
>>   >
>>   >
>>   >
>> ___
>> 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
>>
>>
>> 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] recon-all error

[Ramesh Babu]

Dear Maria,

I am also faced the similar problem when I used Philips DICOM. Then I
converted to nifti format by using dcm2nii tool. It is working fine. You
can also try.

Best
Ramesh

On Mon, Jun 5, 2017 at 7:56 PM, Maria Economou 
wrote:

> Dear FreeSurfer developers,
>
> Sorry for cross-posting, perhaps my previous e-mail was missed.
>
> I've been trying to run recon-all for my first subject and I keep getting
> several errors like:
>
> ERROR: don't know how to get DWI parameters from --Philips Healthcare--
> ERROR: GetDICOMInfo(): dcmGetDWIParams() 1
>
> Too many open files
> ERROR: reading /Applications/freesurfer/FreeSurferColorLUT.txt
> Loading pixel data
> ERROR: /Applications/CONTROLS/147364_Nd_19760623/IM-0001-0001.dcm is not
> a dicom file
>70092 Requested element (18 82) not found in DCM_GetElementVM
>
> I have used the DICOM files from my 3D T1 MPRAGE SENSE images, so I don't
> understand why I get these errors.
>
> This is the command i used: uos$ recon-all -subjid 147364 -i
> /Applications/CONTROLS/147364_Nd_19760623/IM-0001-0001.dcm -all
>
> FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> platform: OS X El Capitan Version 10.11.6
>
> Please find attached the recon-all.log
>
> Many thanks,
> Maria.
>
> ___
> 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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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all -all error end abruptly

[Ramesh Babu]

Dear Bruce,

Two days back I ran 6 image processing simultaneous in different terminal.
Everything finished without any error and took 8.2 hrs (4.5 hrs if I use
only one terminal). But yesterday this problem has happened for the first
time.

I am using Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor with 15.6 GiB
ram, GeForce GT 610/PCIe/SSE2  2GB graphic card. What should I do to
increase my memory?

Thanks
Ramesh

On Mon, Jun 5, 2017 at 7:21 PM, Bruce Fischl 
wrote:

> it looks like you are trying to run the cuda version but your GPU doesn't
> have enough memory
>
> cheers
> Bruce
> On Mon, 5 Jun 2017, Ramesh Babu wrote:
>
> > Dear Expert,
> >
> > recon-all -all process for one subject end abruptly. I have attached the
> > error report file. Please provide me some solution.
> >
> >
> > Thanks
> > Ramesh
> >
> >
> >
> ___
> 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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] recon-all -all error end abruptly

[Ramesh Babu]

Dear Expert,

recon-all -all process for one subject end abruptly. I have attached the
error report file. Please provide me some solution.


Thanks
Ramesh
Sun Jun  4 21:09:32 IST 2017
/mnt/research/freesurfer_analysis/subjects/grp127
/usr/local/freesurfer/bin/recon-all
-all -i grp127_t1.nii -s grp127 -sd subjects -use-gpu
subjid grp127
setenv SUBJECTS_DIR /mnt/research/freesurfer_analysis/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux rameshbabu 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  63592 
maxlocks unlimited
maxsignal63592 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   16326760 232026411793924   33172 221257213636640
Swap:  16669692   016669692


program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/04-15:39:32-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-78-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/04-15:39:32-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-78-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/04-15:39:32-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-78-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/04-15:39:32-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-78-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/04-15:39:32-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-78-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/04-15:39:32-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-78-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/04-15:39:32-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-78-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/04-15:39:32-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-78-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/04-15:39:32-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User: rb  Machine: rameshbabu  Platform: Linux  PlatformVersion: 4.4.0-78-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion

Re: [Freesurfer] cuda-gpu problem

[Ramesh Babu]

Dear Peter,

Thank you very much for your suggestion. You mean to say, 4.6 hrs duration
for recon-all process is because of cpu not gpu? If I run this process
without gpu card then I should get the same speed. Right?
Ok I will remove my graphic card and run directly from mother board
connection which will use only cpu. I just want to know what will be
difference?

If the process will be completed in ~4.6 hrs, then installing higher end
graphic must reduce the duration further. If so then I will go for higher
end graphic card.

Thanks
Ramesh



On Wed, May 24, 2017 at 9:38 PM, Senften, Peter 
wrote:

> Hi Ramesh,
>
> I do not know if you have considered this at all but I at least wanted to
> bring it to your attention. If you have please disregard.
>
> I've been doing I.T. for over 20 years and the Nvidia card you have listed
> is the Geforce 610 concerns me that all of the effort you're going through
> won't be worth it in the end. It is several years old, released in May of
> 2012, and is a very basic card. I would be surprised if the CUDA code path
> runs quicker than your CPU because, even when it was released, it was the
> lowest end card of the 600 series. Unless you have a higher end Nvidia
> card, such as the 970, 980, 1060 (or higher) your CPU will very likely be
> faster in the recon-all process.
>
> Best,
>
> Peter
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Ramesh Babu [
> mgrameshbabu2...@gmail.com]
> *Sent:* Wednesday, May 24, 2017 3:51 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] cuda-gpu problem
>
> Dear Richard,
> This command recon-all -all -i grp237_t1.nii -s grp237 -sd grp237
> -use-gpu -itkthreat 4 took 5.18 hrs and recon-all -all -i grp237_t1.nii
> -s grp237 -sd grp237 -use-gpu -openmp 4 took 4.69 hrs without any error.
>
> Thank you very much for your suggestions.
>
> Ramesh
>
>
>
> On Tue, May 23, 2017 at 3:37 PM, R Edgar  wrote:
>
>> On 23 May 2017 at 01:10, Ramesh Babu  wrote:
>>
>> > I have one question. When use -use-gpu flag, can I use -itkthreads 8 or
>> -use
>> > openmp 8 flag?
>>
>> That's not something I've tested. I think that OpenMP at least is OK
>> (things will run in parallel on the CPU or the GPU.
>>
>> Richard
>> ___
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>>
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] Installing and enabling cuda

[Ramesh Babu]

Dear Richard,

There is some response for cudadetect command which I have pated in earlier
mail. But no ./cudadetect file.

rb@rameshbabu:~$ ./cudadetect
bash: ./cudadetect: No such file or directory

I have nvcc file in /usr/local/cuda/bin but still not located.

rb@rameshbabu:~$ which nvcc  (no response)
rb@rameshbabu:~$ ll /usr/local/cuda/bin/
total 31836
drwxr-xr-x  3 root root4096 May 19 19:56 ./
drwxr-xr-x 16 root root4096 May 19 19:56 ../
-rwxr-xr-x  1 root root   63288 May 19 19:56 bin2c*
lrwxrwxrwx  1 root root   4 May 19 19:56 computeprof -> nvvp*
drwxr-xr-x  2 root root4096 May 19 19:56 crt/
-rwxr-xr-x  1 root root 3240648 May 19 19:56 cudafe*
-rwxr-xr-x  1 root root 2904184 May 19 19:56 cudafe++*
-rwxr-xr-x  1 root root 5698534 May 19 19:56 cuda-gdb*
-rwxr-xr-x  1 root root  170664 May 19 19:56 cuda-memcheck*
-rwxr-xr-x  1 root root 6460832 May 19 19:56 cuobjdump*
-rwxr-xr-x  1 root root  164992 May 19 19:56 fatbin*
-rwxr-xr-x  1 root root  125584 May 19 19:56 fatbinary*
-rwxr-xr-x  1 root root   58680 May 19 19:56 filehash*
-rwxr-xr-x  1 root root 210 May 19 19:56 nsight*
-rwxr-xr-x  1 root root  160576 May 19 19:56 nvcc*
-rw-r--r--  1 root root 306 May 19 19:56 nvcc.profile
-rwxr-xr-x  1 root root 5729960 May 19 19:56 nvlink*
-rwxr-xr-x  1 root root 2166448 May 19 19:56 nvprof*
-rwxr-xr-x  1 root root 206 May 19 19:56 nvvp*
-rwxr-xr-x  1 root root 5600776 May 19 19:56 ptxas*

rb@rameshbabu:~$ nvcc --version
The program 'nvcc' is currently not installed. You can install it by typing:
sudo apt install nvidia-cuda-toolkit


rb@rameshbabu:~$ locate libcudart
/usr/local/MATLAB/R2017a/bin/glnxa64/libcudart.so.8.0
/usr/local/MATLAB/R2017a/bin/glnxa64/libcudart.so.8.0.44
/usr/local/cuda-5.0/lib/libcudart.so
/usr/local/cuda-5.0/lib/libcudart.so.5.0
/usr/local/cuda-5.0/lib/libcudart.so.5.0.35
/usr/local/cuda-5.0/lib64/libcudart.so
/usr/local/cuda-5.0/lib64/libcudart.so.5.0
/usr/local/cuda-5.0/lib64/libcudart.so.5.0.35
/usr/local/freesurfer/MCRv80/bin/glnxa64/libcudart.so.4
/usr/local/freesurfer/MCRv80/bin/glnxa64/libcudart.so.4.2.9

As far as I know, freesurfer supports cuda-5 and it requires
libcudart.so-5.0. That's why I have installed cuda-5. How did you enable
freesurfer with cuda-8?

Thanks
Ramesh


On Thu, May 25, 2017 at 5:42 AM, R Edgar  wrote:

> On 24 May 2017 at 00:36, Ramesh Babu  wrote:
>
> > Now I am getting confusion, really which version of cuda I have?. Because
> > when I give these command "cudadetect" nvcc -V, and cat
> > /usr/local/cuda/version.txt  I am getting different answers.
> >
> > rb@rameshbabu:~$ cudadetect
> > Detecting CUDA... There is 1 device supporting CUDA:
> >
> > Device 0: "GeForce GT 610"
> >   CUDA Driver Version:   8.0
> >   CUDA Runtime Version:  5.0
> >   CUDA Capability Major revision number: 2
> >   CUDA Capability Minor revision number: 1
> >   Total amount of global memory: 2080440320 bytes
> >   Number of multiprocessors: 1
> >   Number of cores:   32
> >   Total amount of constant memory:   65536 bytes
> >   Total amount of shared memory per block:   49152 bytes
> >   Total number of registers available per block: 32768
> >   Warp size: 32
> >   Maximum number of threads per block:   1024
> >   Maximum sizes of each dimension of a block:1024 x 1024 x 64
> >   Maximum sizes of each dimension of a grid: 65535 x 65535 x 65535
> >   Maximum memory pitch:  2147483647 bytes
> >   Texture alignment: 512 bytes
> >   Clock rate:1.62 GHz
> >   Concurrent copy and execution: Yes
> >   Run time limit on kernels: Yes
> >   Integrated:No
> >   Support host page-locked memory mapping:   Yes
> >   Compute mode:  Default (multiple host
> > threads can use this device simultaneously)
>
> cudadetect is installed by freesurfer. For me, the output starts:
> [rge21@cudastation gpu_utils]$ ./cudadetect
> Detecting CUDA... There is 1 device supporting CUDA:
>
> Device 0: "Quadro K1200"
>   CUDA Driver Version:   8.0
>   CUDA Runtime Version:  8.0
>   CUDA Capability Major revision number: 5
>   CUDA Capability Minor revision number: 0
>
> > rb@rameshbabu:~$ cat /usr/local/cuda/version.txt
> > cat: /usr/local/cuda/version.txt: No such file or directory
> >
> > rb@rameshbabu:~$ nvcc -V
> > The program '

Re: [Freesurfer] cuda-gpu problem

[Ramesh Babu]

Dear Richard,
This command recon-all -all -i grp237_t1.nii -s grp237 -sd grp237 -use-gpu
-itkthreat 4 took 5.18 hrs and recon-all -all -i grp237_t1.nii -s grp237
-sd grp237 -use-gpu -openmp 4 took 4.69 hrs without any error.

Thank you very much for your suggestions.

Ramesh



On Tue, May 23, 2017 at 3:37 PM, R Edgar  wrote:

> On 23 May 2017 at 01:10, Ramesh Babu  wrote:
>
> > I have one question. When use -use-gpu flag, can I use -itkthreads 8 or
> -use
> > openmp 8 flag?
>
> That's not something I've tested. I think that OpenMP at least is OK
> (things will run in parallel on the CPU or the GPU.
>
> Richard
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Installing and enabling cuda

[Ramesh Babu]

Dear Richard,
Now I am getting confusion, really which version of cuda I have?. Because
when I give these command "cudadetect" nvcc -V, and cat
/usr/local/cuda/version.txt  I am getting different answers.



rb@rameshbabu:~$ cudadetect
Detecting CUDA... There is 1 device supporting CUDA:

Device 0: "GeForce GT 610"
  CUDA Driver Version:   8.0
  CUDA Runtime Version:  5.0
  CUDA Capability Major revision number: 2
  CUDA Capability Minor revision number: 1
  Total amount of global memory: 2080440320 bytes
  Number of multiprocessors: 1
  Number of cores:   32
  Total amount of constant memory:   65536 bytes
  Total amount of shared memory per block:   49152 bytes
  Total number of registers available per block: 32768
  Warp size: 32
  Maximum number of threads per block:   1024
  Maximum sizes of each dimension of a block:1024 x 1024 x 64
  Maximum sizes of each dimension of a grid: 65535 x 65535 x 65535
  Maximum memory pitch:  2147483647 bytes
  Texture alignment: 512 bytes
  Clock rate:1.62 GHz
  Concurrent copy and execution: Yes
  Run time limit on kernels: Yes
  Integrated:No
  Support host page-locked memory mapping:   Yes
  Compute mode:  Default (multiple host
threads can use this device simultaneously)


rb@rameshbabu:~$ cat /usr/local/cuda/version.txt
cat: /usr/local/cuda/version.txt: No such file or directory

rb@rameshbabu:~$ nvcc -V
The program 'nvcc' is currently not installed. You can install it by
typing: sudo apt install nvidia-cuda-toolkit

The first command reports that I have CUDA Driver Version: 8.0 and CUDA
Runtime Version: 5.0, but why I am not getting any report for other two
commands.

Please provide a solution.

Thanks
Ramesh

On Tue, May 23, 2017 at 3:38 PM, R Edgar  wrote:

> On 23 May 2017 at 01:13, Ramesh Babu  wrote:
>
> > Ok. I will try cuda 8.0 and let you know the result. Should I install
> cuda 5
> > before installing cuda 8? or Can I run both?
>
> You'll only be able to have one version of the CUDA driver, but you
> should be able to have multiple CUDA SDKs.
>
> Richard
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>
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> is
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Re: [Freesurfer] Installing and enabling cuda

[Ramesh Babu]

Dear Richard,

Ok. I will try cuda 8.0 and let you know the result. Should I install cuda
5 before installing cuda 8? or Can I run both?

Thanks
Ramesh

On Tue, May 23, 2017 at 1:54 AM, R Edgar  wrote:

> On 22 May 2017 at 08:44, Ramesh Babu  wrote:
>
> > After compiling in the same way as given in the webpage, I couldn't
> reboot.
> > It was showing a message that "running low graphic mode". It was not
> opening
> > the desktop. Then through ctrl+alt+f1, I uninstalled nvida and cuda.
> Then I
> > could boot the system.
> >
> > Finally I have installed both cuda and nvidia after going through many
> web
> > sources.
> > I have installed NVIDIA drive through additional driver option in Ubuntu
> > software & update centre. It installed recommended nvidia driver.
> >
> > For cuda installation I followed these scripts,
> > [chmod +x cuda_5.0.35_linux_64_ubuntu11.10-1.run
> > sudo ./cuda_5.0.35_linux_64_ubuntu11.10-1.run --override
> > sudo gedit ~/.bashrc
> > sudo nano /usr/local/cuda/include/host_config.h
> >
> > line: 115 comment out error
> > //#error -- unsupported GNU version! gcc versions later than 4.9 are not
> > supported!
> >
> > rsync -av /usr/local/cuda/samples ]
> >
> > I need your help to check whether cuda is connected with freesurfer. How
> to
> > check this.
>
> Compiling freesurfer should not result in a non-booting computer.
>
> I'm afraid I wasn't using CUDA around v5. On my CentOS box, I
> installed the SDK using yum (i.e. rpm), and it upgraded itself to CUDA
> 8.0 when that came out.
>
> Is there some reason you can't go to CUDA 8.0?
>
> Richard
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Re: [Freesurfer] cuda-gpu problem

[Ramesh Babu]

Dear Richard,

Yesterday I performed single subject analysis with -use-gpu flag and
allowed to take its own time to complete. It's get completed within 5.8
hrs. Yes you are correct. I should not interrupt before a final output. And
I have realized that gpu and cpu outputs on the terminal are not similar.
Thank you for your feedback.

I have one question. When use -use-gpu flag, can I use -itkthreads 8 or
-use openmp 8 flag?

Thanks
Ramesh




On Tue, May 23, 2017 at 1:51 AM, R Edgar  wrote:

> On 22 May 2017 at 07:39, Ramesh Babu  wrote:
>
> > The following last line get repeated same way except (%) in the second
> line
> > pasted below. On the third line "Did not call MRIsetResolution", is it
> error
> > or normal process? Since repeated many times I thought there is some
> error.
> >
> > PutOnGPU: Did not reset gca in dst
> > 0270: dt=9.072001, rms=0.557 (0.021%), neg=0, invalid=762
> > LabelTerm: Did not call MRIsetResolution
>
> That's completely normal - it was sort of an aide-memoire for myself.
> Should things start messing up in interesting ways, that might be
> something to go and check (at the time I did the port, it was a no-op
> for the command I was running). So long as the
> nnn: dt=
> lines are popping out OK, it's running.
>
> Richard
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Re: [Freesurfer] Installing and enabling cuda

[Ramesh Babu]

Dear Richard,

After compiling in the same way as given in the webpage, I couldn't reboot.
It was showing a message that "running low graphic mode". It was not
opening the desktop. Then through ctrl+alt+f1, I uninstalled nvida and
cuda. Then I could boot the system.

Finally I have installed both cuda and nvidia after going through many web
sources.
I have installed NVIDIA drive through additional driver option in Ubuntu
software & update centre. It installed recommended nvidia driver.

For cuda installation I followed these scripts,
[chmod +x cuda_5.0.35_linux_64_ubuntu11.10-1.run
sudo ./cuda_5.0.35_linux_64_ubuntu11.10-1.run --override
sudo gedit ~/.bashrc
sudo nano /usr/local/cuda/include/host_config.h

line: 115 comment out error
//#error -- unsupported GNU version! gcc versions later than 4.9 are
not supported!

rsync -av /usr/local/cuda/samples ]

I need your help to check whether cuda is connected with freesurfer. How to
check this.


Thanks
Ramesh



On Mon, May 22, 2017 at 2:51 PM, R Edgar  wrote:

> On 21 May 2017 at 23:40, Ramesh Babu  wrote:
>
> > Thank you for your reply. I tried to compile by looking FAQ about CUDA in
> > Ubuntu Ask, but it is get corrupted and I am forced to uninstall both
> NVIDIA
> > driver and CUDA.  I need help to compile it. Can I get some guidance or
> > manual?
>
> How do you mean corrupted?
>
> I have found it necessary to edit the configure script which is
> generated, and to manually pass it the path to nvcc, but I don't
> believe I've seen something get corrupted before.
>
> Regards,
>
> Richard
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Re: [Freesurfer] cuda-gpu problem

[Ramesh Babu]

Dear Richard,

The following last line get repeated same way except (%) in the second line
pasted below. On the third line "Did not call MRIsetResolution", is it
error or normal process? Since repeated many times I thought there is some
error.

PutOnGPU: Did not reset gca in dst
0270: dt=9.072001, rms=0.557 (0.021%), neg=0, invalid=762
LabelTerm: Did not call MRIsetResolution

Shall I repeat the process again with -use-gpu flag?

I hope mri_ca_register_cuda is working fine.

$ mri_ca_register_cuda
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2012 NVIDIA Corporation
Built on Fri_Sep_21_17:28:58_PDT_2012
Cuda compilation tools, release 5.0, V0.2.1221

Driver : 8.0
Runtime : 5.0

Acquiring CUDA device
Using default device
CUDA device: GeForce GT 610
Help

NAME
mri_ca_register

SYNOPSIS
mri_ca_register   

(didn't past complete output)


On Mon, May 22, 2017 at 2:55 PM, R Edgar  wrote:

> On 22 May 2017 at 03:10, Ramesh Babu  wrote:
>
> > I have attached two documents. One document contains report with -use-gpu
> > flag which I have interrupted and another document is without -use-gpu
> flag,
> > completed without any error. Wherever report differ from normal run I
> have
> > highlighted. Please have a look and give your suggestion.
>
> I can see that the "with GPU" trace ends in a run of mri_ca_register
> rather suddenly, but I do not see any errors in that trace. What
> happened? Did mri_ca_register_cuda crash? It didn't reach the same
> step count as the CPU trace.
>
> Richard
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Re: [Freesurfer] Installing and enabling cuda

[Ramesh Babu]

Dear Richard,
Thank you for your reply. I tried to compile by looking FAQ about CUDA in
Ubuntu Ask, but it is get corrupted and I am forced to uninstall both
NVIDIA driver and CUDA.  I need help to compile it. Can I get some guidance
or manual?

Thanks
Ramesh


On Sun, May 21, 2017 at 2:18 AM, R Edgar  wrote:

> On 16 May 2017 at 23:10, Ramesh Babu  wrote:
>
> > I have come across that I have freesurfer support cuda version 5, but I
> have
> > already installed latest version.
> > Can I use latest version for freeesurfer or should I install version 5?
> > Since I am not expert in this field I need guidance to remove latest
> version
> > of cuda and installing and enabling version 5.
> >
> > Your help will be appreciated.
> >
> > PC details:
> > I am using Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor with 15.6 GiB
> > ram, GeForce GT 610/PCIe/SSE2 graphic card.
>
> I have CUDA 8 on my machine, and it seems to run quite happily
> (although I do compile myself). I don't believe that NVIDIA have made
> any breaking changes in the CUDA SDK, although looking at things
> recently, some might be coming.
>
> HTH,
>
> Richard
>
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[Freesurfer] Installing and enabling cuda

[Ramesh Babu]

Dear Expert,

I have come across that I have freesurfer support cuda version 5, but I
have already installed latest version.
Can I use latest version for freeesurfer or should I install version 5?
Since I am not expert in this field I need guidance to remove latest
version of cuda and installing and enabling version 5.

Your help will be appreciated.

PC details:
I am using Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor with 15.6 GiB
ram, GeForce GT 610/PCIe/SSE2 graphic card.

Thanks
RB
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Re: [Freesurfer] Hippo-subfiled Need Help

[Ramesh Babu]

Dear Eugenio,
Thanks for your suggestion. What about the quality if segmented image which
I have attached.
Please give your suggestions on the attached hippo-seg.
Thanks
Ramesh

On Mon, May 1, 2017 at 12:23 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Dear Ramesh,
>
> The subfield segmentations requires running recon-all -all first. But you
> can greatly speed up the execution with the openmp option. Also, you can
> try running two subjects simultaneously, but only for the recon-all -all
> part (the subfields use more memory and might crash).
>
> Cheers,
>
> /Eugenio
>
>
> Juan Eugenio Iglesias
>
> Translational Imaging Group
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ramesh Babu <
> mgrameshbabu2...@gmail.com>
> *Sent:* Saturday, April 29, 2017 9:46:24 AM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] Hippo-subfiled Need Help
>
> Dear Experts,
>
> I ave done hippocampal subfield segmentation by using 1x1x1 t1 scan.
> Please see the attached image and give your suggestions.
>
> It took nearly 7 hrs 10 min. to complete hippo-subfield segmentation for
> one scan by using the command
>
> recon-all -i grp205_t1.nii -s grp205 -sd grp205 -all
>
> Started at Wed Apr 26 11:03:34 IST 2017
> Ended   at Wed Apr 26 17:17:35 IST 2017
> #@#%# recon-all-run-time-hours 6.234
> recon-all -s grp205 finished without error at Wed Apr 26 17:17:35 IST 2017
> done
>
> Then for hipposubfield,
>
> recon-all -s grp205 -sd grp205 -hippocampal-subfields-T1
>
>
> I want to run for 40 scans grp-1 20 scans and grp-2 20 scans. How to
> modify in the command. Since it is taking long time I want to run 10 scans
> n give rest again 10 scans. Can I do so?
>
> I am15.6 GiB ram, Intel® Core™ i7-4790 CPU @ 3.60GHz × 8 processor,
> GeForce GT 610/PCIe/SSE2 graphic card.It is octa core processor. Can I
> run 8 analysis simultaneously (in 8 separate terminal?).
>
> Your suggestion will be helpful to me to proceed further.
>
> Thanks
> RB
>
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Re: [Freesurfer] Need help to run freesurfer

[Ramesh Babu]

Dear Z K,

I have downloaded again by using the following command on the terminal;

wget http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz

Then md5sum check;
 md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
d49e9dd61d6467f65b9582bddec653a4  freesurfer-Linux-centos6_x86_
64-stable-pub-v6.0.0.tar.gz

pc@RB:/usr/local$ ls freesurfer/
ASegStatsLUT.txtFreeSurferEnv.sh  SetUpFreeSurfer.csh
AUTHORS fsafd SetUpFreeSurfer.sh
average fsfastSimple_surface_labels2009.txt
bin lib   sources.csh
build-stamp.txt LICENSE   sources.sh
datamatlabsubjects
DefectLUT.txt   mni   tkmeditParcColorsCMA
diffusion   NOTICEtktools
docsREADMEtrctrain
FreeSurferColorLUT.txt  SegmentNoLUT.txt  VERSION
FreeSurferEnv.csh   sessions  WMParcStatsLUT.txt


All the files have been downloaded. Working fine.

Whenever I open my terminal it opens with the following message all the
time. How to avoid it?

bash: /usr/local/freesurfer/SetUpFreeSurfer.csh: line 43: syntax error:
unexpected end of file
 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/share/fsl/5.0
pc@RB:~$


Thanks
RB



On Sat, Apr 22, 2017 at 9:50 AM, Ramesh Babu 
wrote:

> Dear ZK,
>
> I have done md5sum check. I got the following message. How to confirm it
> is complete or not?
>
> pc@RB:~/Downloads$ md5sum 
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
>
> 5362fc776145b06ded219f42af4a8207  freesurfer-Linux-centos6_x86_
> 64-stable-pub-v6.0.0.tar.gz
>
>
> Thanks
> RB
>
> On Thu, Apr 20, 2017 at 7:32 PM, Z K  wrote:
>
>> I just did a test by downloading and extracting the tar, and I got all
>> the expected files:
>>
>> /usr/local/fstemp/freesurfer/tkmeditParcColorsCMA
>> /usr/local/fstemp/freesurfer/mni
>> /usr/local/fstemp/freesurfer/sources.csh
>> /usr/local/fstemp/freesurfer/docs
>> /usr/local/fstemp/freesurfer/Simple_surface_labels2009.txt
>> /usr/local/fstemp/freesurfer/NOTICE
>> /usr/local/fstemp/freesurfer/FreeSurferColorLUT.txt
>> /usr/local/fstemp/freesurfer/DefectLUT.txt
>> /usr/local/fstemp/freesurfer/subjects
>> /usr/local/fstemp/freesurfer/LICENSE
>> /usr/local/fstemp/freesurfer/fsafd
>> /usr/local/fstemp/freesurfer/ASegStatsLUT.txt
>> /usr/local/fstemp/freesurfer/diffusion
>> /usr/local/fstemp/freesurfer/average
>> /usr/local/fstemp/freesurfer/bin
>> /usr/local/fstemp/freesurfer/SetUpFreeSurfer.sh
>> /usr/local/fstemp/freesurfer/SegmentNoLUT.txt
>> /usr/local/fstemp/freesurfer/README
>> /usr/local/fstemp/freesurfer/sources.sh
>> /usr/local/fstemp/freesurfer/data
>> /usr/local/fstemp/freesurfer/SetUpFreeSurfer.csh
>> /usr/local/fstemp/freesurfer/tktools
>> /usr/local/fstemp/freesurfer/FreeSurferEnv.sh
>> /usr/local/fstemp/freesurfer/fsfast
>> /usr/local/fstemp/freesurfer/WMParcStatsLUT.txt
>> /usr/local/fstemp/freesurfer/VERSION
>> /usr/local/fstemp/freesurfer/build-stamp.txt
>> /usr/local/fstemp/freesurfer/trctrain
>> /usr/local/fstemp/freesurfer/lib
>> /usr/local/fstemp/freesurfer/FreeSurferEnv.csh
>> /usr/local/fstemp/freesurfer/AUTHORS
>> /usr/local/fstemp/freesurfer/matlab
>> /usr/local/fstemp/freesurfer/sessions
>>
>>
>> Perhaps your file was not yet complete, or it was corrupted in some way.
>> The md5sum of the tarball is 'd49e9dd61d6467f65b9582bddec653a4' which
>> you can get by typing:
>>
>>md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
>>
>>
>> On 04/20/2017 08:04 AM, Ramesh Babu wrote:
>> > Dear Experts,
>> >
>> > I have installed in /usr/local/freesurfer. I am trying to follow the
>> > command given in the freesurfer web page.
>> >
>> > $> export FREESURFER_HOME=/usr/local/freesurfer $> source
>> > $FREESURFER_HOME/SetUpFreeSurfer.sh
>> >
>> > But I could not figure out the .sh file in the freesurfer folder. Please
>> > see the list of files in the freesurfer folder given below.
>> >
>> > List of files in the freesurfer folder;
>> >
>> > /usr/local/freesurfer/average
>> > /usr/local/freesurfer/fsafd
>> > /usr/local/freesurfer/

Re: [Freesurfer] Need help to run freesurfer

[Ramesh Babu]

Dear ZK,

I have done md5sum check. I got the following message. How to confirm it is
complete or not?

pc@RB:~/Downloads$ md5sum
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
5362fc776145b06ded219f42af4a8207
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz


Thanks
RB

On Thu, Apr 20, 2017 at 7:32 PM, Z K  wrote:

> I just did a test by downloading and extracting the tar, and I got all
> the expected files:
>
> /usr/local/fstemp/freesurfer/tkmeditParcColorsCMA
> /usr/local/fstemp/freesurfer/mni
> /usr/local/fstemp/freesurfer/sources.csh
> /usr/local/fstemp/freesurfer/docs
> /usr/local/fstemp/freesurfer/Simple_surface_labels2009.txt
> /usr/local/fstemp/freesurfer/NOTICE
> /usr/local/fstemp/freesurfer/FreeSurferColorLUT.txt
> /usr/local/fstemp/freesurfer/DefectLUT.txt
> /usr/local/fstemp/freesurfer/subjects
> /usr/local/fstemp/freesurfer/LICENSE
> /usr/local/fstemp/freesurfer/fsafd
> /usr/local/fstemp/freesurfer/ASegStatsLUT.txt
> /usr/local/fstemp/freesurfer/diffusion
> /usr/local/fstemp/freesurfer/average
> /usr/local/fstemp/freesurfer/bin
> /usr/local/fstemp/freesurfer/SetUpFreeSurfer.sh
> /usr/local/fstemp/freesurfer/SegmentNoLUT.txt
> /usr/local/fstemp/freesurfer/README
> /usr/local/fstemp/freesurfer/sources.sh
> /usr/local/fstemp/freesurfer/data
> /usr/local/fstemp/freesurfer/SetUpFreeSurfer.csh
> /usr/local/fstemp/freesurfer/tktools
> /usr/local/fstemp/freesurfer/FreeSurferEnv.sh
> /usr/local/fstemp/freesurfer/fsfast
> /usr/local/fstemp/freesurfer/WMParcStatsLUT.txt
> /usr/local/fstemp/freesurfer/VERSION
> /usr/local/fstemp/freesurfer/build-stamp.txt
> /usr/local/fstemp/freesurfer/trctrain
> /usr/local/fstemp/freesurfer/lib
> /usr/local/fstemp/freesurfer/FreeSurferEnv.csh
> /usr/local/fstemp/freesurfer/AUTHORS
> /usr/local/fstemp/freesurfer/matlab
> /usr/local/fstemp/freesurfer/sessions
>
>
> Perhaps your file was not yet complete, or it was corrupted in some way.
> The md5sum of the tarball is 'd49e9dd61d6467f65b9582bddec653a4' which
> you can get by typing:
>
>md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
>
>
> On 04/20/2017 08:04 AM, Ramesh Babu wrote:
> > Dear Experts,
> >
> > I have installed in /usr/local/freesurfer. I am trying to follow the
> > command given in the freesurfer web page.
> >
> > $> export FREESURFER_HOME=/usr/local/freesurfer $> source
> > $FREESURFER_HOME/SetUpFreeSurfer.sh
> >
> > But I could not figure out the .sh file in the freesurfer folder. Please
> > see the list of files in the freesurfer folder given below.
> >
> > List of files in the freesurfer folder;
> >
> > /usr/local/freesurfer/average
> > /usr/local/freesurfer/fsafd
> > /usr/local/freesurfer/fsfast
> > /usr/local/freesurfer/lib
> > /usr/local/freesurfer/sessions
> > /usr/local/freesurfer/tktools
> > /usr/local/freesurfer/trctrain
> > /usr/local/freesurfer/DefectLUT.txt
> > /usr/local/freesurfer/FreeSurferColorLUT.txt
> > /usr/local/freesurfer/FreeSurferEnv.csh
> > /usr/local/freesurfer/LICENSE
> > /usr/local/freesurfer/SetUpFreeSurfer.csh
> > /usr/local/freesurfer/sources.csh
> > /usr/local/freesurfer/sources.sh
> > /usr/local/freesurfer/tkmeditParcColorsCMA
> > /usr/local/freesurfer/VERSION
> > /usr/local/freesurfer/WMParcStatsLUT.txt
> >
> > You can notice that there is no SetUpFreeSurfer.sh file.
> >
> > Details about my pc;
> >
> >
> > Ubuntu 16.04 LTS, 64 bit is installed. Running w8.1 via virtual box.
> > Freesurfer is installed in Ubuntu OS.
> >
> >
> > I am using bash shell.
> >
> > pc@RB:~$ echo $0
> > bash
> >
> > pc@RB:~$ echo $SHELL
> > /bin/bash
> >
> > pc@RB:~$ ps -p "$$"
> >   PID TTY  TIME CMD
> >  3706 pts/100:00:00 bash
> >
> > Need your help to run freesurfer in my pc.
> >
> >
> > Thanks in advance
> >
> > Ramesh
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.or

[Freesurfer] Need help to run freesurfer

[Ramesh Babu]

Dear Experts,

I have installed in /usr/local/freesurfer. I am trying to follow the
command given in the freesurfer web page.

$> export FREESURFER_HOME=/usr/local/freesurfer
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh

But I could not figure out the .sh file in the freesurfer folder.
Please see the list of files in the freesurfer folder given below.

List of files in the freesurfer folder;

/usr/local/freesurfer/average
/usr/local/freesurfer/fsafd
/usr/local/freesurfer/fsfast
/usr/local/freesurfer/lib
/usr/local/freesurfer/sessions
/usr/local/freesurfer/tktools
/usr/local/freesurfer/trctrain
/usr/local/freesurfer/DefectLUT.txt
/usr/local/freesurfer/FreeSurferColorLUT.txt
/usr/local/freesurfer/FreeSurferEnv.csh
/usr/local/freesurfer/LICENSE
/usr/local/freesurfer/SetUpFreeSurfer.csh
/usr/local/freesurfer/sources.csh
/usr/local/freesurfer/sources.sh
/usr/local/freesurfer/tkmeditParcColorsCMA
/usr/local/freesurfer/VERSION
/usr/local/freesurfer/WMParcStatsLUT.txt

You can notice that there is no SetUpFreeSurfer.sh file.

Details about my pc;


Ubuntu 16.04 LTS, 64 bit is installed. Running w8.1 via virtual box.
Freesurfer is installed in Ubuntu OS.


I am using bash shell.

pc@RB:~$ echo $0
bash

pc@RB:~$ echo $SHELL
/bin/bash

pc@RB:~$ ps -p "$$"
  PID TTY  TIME CMD
 3706 pts/100:00:00 bash

Need your help to run freesurfer in my pc.


Thanks in advance

Ramesh
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] New to freesurfer Needhelp to install in Ubuntu 16 lts

[Ramesh Babu]

Dear Bruce,
I am using bash shell. Please see the further details below.

pc@RB:~$ echo $0
bash
pc@RB:~$ echo $SHELL
/bin/bash
pc@RB:~$ ps -p "$$"
  PID TTY  TIME CMD
 3706 pts/100:00:00 bash

List of fails in the freesurfer folder;

/usr/local/freesurfer/average
/usr/local/freesurfer/fsafd
/usr/local/freesurfer/fsfast
/usr/local/freesurfer/lib
/usr/local/freesurfer/sessions
/usr/local/freesurfer/tktools
/usr/local/freesurfer/trctrain
/usr/local/freesurfer/DefectLUT.txt
/usr/local/freesurfer/FreeSurferColorLUT.txt
/usr/local/freesurfer/FreeSurferEnv.csh
/usr/local/freesurfer/LICENSE
/usr/local/freesurfer/SetUpFreeSurfer.csh
/usr/local/freesurfer/sources.csh
/usr/local/freesurfer/sources.sh
/usr/local/freesurfer/tkmeditParcColorsCMA
/usr/local/freesurfer/VERSION
/usr/local/freesurfer/WMParcStatsLUT.txt

You can notice that there is no SetUpFreeSurfer.sh files.

Details about my pc;

Ubuntu 16.04 LTS, 64 bit is installed. Running w8.1 via virtual box.
Memory - 16GB ram
Processor- Intel® Core™ i7-4790 CPU @ 3.60GHz × 8
Graphics - GeForce GT 610/PCIe/SSE2


Thanks
Ramesh

On Fri, Apr 14, 2017 at 8:13 PM, Bruce Fischl 
wrote:

> Hi Ramesh
>
> you need to tell us what shell you are running.
>
> cheers
> Bruce
> On Fri, 14 Apr 2017, Ramesh
> Babu wrote:
>
> > Dear Expert,
> >
> > I am new member of this freesurfer mailing list. I just downloaded
> > freesurfer package and installed in /usr/local/freesurfer.
> >
> > I am trying to follow the command given in the freesurfer web page.
> >
> > $> export FREESURFER_HOME=/usr/local/freesurfer
> > $> source $FREESURFER_HOME/SetUpFreeSurfer.sh
> >
> > But I could not figure out the .sh file in the freesurfer folder.
> Instead th
> > ere is .csh file. Can I change it as
> >
> > "$> source $FREESURFER_HOME/SetUpFreeSurfer.csh". Since I have started
> using
> >  Ubuntu recently, I am not not sure whether I can change it.
> >
> > Need your help to install freesurfer in my pc.
> > Thanks in advance
> >
> > Ramesh
> >
> >
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

[Freesurfer] New to freesurfer Needhelp to install in Ubuntu 16 lts

[Ramesh Babu]

Dear Expert,

I am new member of this freesurfer mailing list. I just downloaded
freesurfer package and installed in /usr/local/freesurfer.

I am trying to follow the command given in the freesurfer web page.

$> export FREESURFER_HOME=/usr/local/freesurfer
$> source $FREESURFER_HOME/SetUpFreeSurfer.sh

But I could not figure out the .sh file in the freesurfer folder.
Instead there is .csh file. Can I change it as

"$> source $FREESURFER_HOME/SetUpFreeSurfer.csh". Since I have started
using Ubuntu recently, I am not not sure whether I can change it.

Need your help to install freesurfer in my pc.

Thanks in advance

Ramesh
___
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.