[Freesurfer] recon-all on group

[Muhammad Naveed Iqbal Qureshi]

Can we apply recon-all on a group of subjects simultaneously?
My system has good enough processing power to preprocess 40 subjects at a time, 
but I have to open 40 terminal windows for doing it now.
I need an efficient way to do it.
 
Any suggestions?  



Best Regards,

Muhammad
Naveed Iqbal Qureshi

P please don't print this e-mail unless
you really need to

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Re: [Freesurfer] converting .nii to .mgz

[Borzello, Mia]

Hi Bruce, 

Thanks for getting back to me so quickly! 
I just tried that and got the following error: 
reading from ct.anat.nii...
niiRead(): error opening file 
/autofs/space/huygens_001/users/mia/subjects/ct.anat.nii

I'm wondering if the nifti file is possibly corrupted. Is there a way to check 
this?

Thanks so much, 
Mia 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, January 19, 2015 10:38 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] converting .nii to .mgz

Hi Mia
If all you want to do is convert try

mri_convert ct.anat.nii ct.anat.mgz

Cheers
Bruce



> On Jan 19, 2015, at 10:33 PM, Borzello, Mia  wrote:
>
> Hi Freesurfers,
>
> I'm looking at Freesurfer files from are from years ago trying to look at the 
> ct.anat file. Unfortunately, i have the nifti file and not the mgz file, so 
> I'm wondering if there is a way to create it. In trying to find an answer 
> online, I found this: 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html
> I tried that but got an error. It may be a syntax error; this was my command 
> line: recon-all -i 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  MG17_SurferOutput 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
>
>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
>
> RedHat release: CentOS release 6.5 (Final)
>
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
>
> NMR Center info (/space/freesurfer exists):
>
>  machine: huygens
>
>  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
>
>  PWD: /autofs/space/huygens_001/users/mia/subjects
>
>  ssh huygens
>  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>  cd /autofs/space/huygens_001/users/mia/subjects
>
>
> 1) MG17
> 2) recon-all -i 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  MG17_SurferOutput 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
> 3) ERROR: Flag 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  unrecognized.
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  MG17_SurferOutput 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s  exited with ERRORS at Mon Jan 19 22:27:18 EST 2015
>
> For more details, see the log file
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> Thanks so much,
> Mia
> ___
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>
>

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Re: [Freesurfer] converting .nii to .mgz

[Bruce Fischl]

Hi Mia
If all you want to do is convert try

mri_convert ct.anat.nii ct.anat.mgz

Cheers
Bruce



> On Jan 19, 2015, at 10:33 PM, Borzello, Mia  wrote:
> 
> Hi Freesurfers, 
> 
> I'm looking at Freesurfer files from are from years ago trying to look at the 
> ct.anat file. Unfortunately, i have the nifti file and not the mgz file, so 
> I'm wondering if there is a way to create it. In trying to find an answer 
> online, I found this: 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html
> I tried that but got an error. It may be a syntax error; this was my command 
> line: recon-all -i 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  MG17_SurferOutput 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
> 
> 
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
> 
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
> 
> RedHat release: CentOS release 6.5 (Final)
> 
> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64
> 
> NMR Center info (/space/freesurfer exists):
> 
>  machine: huygens
> 
>  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects
> 
>  PWD: /autofs/space/huygens_001/users/mia/subjects
> 
>  ssh huygens
>  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
>  cd /autofs/space/huygens_001/users/mia/subjects
> 
> 
> 1) MG17
> 2) recon-all -i 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  MG17_SurferOutput 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
> 3) ERROR: Flag 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  unrecognized.
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii
>  MG17_SurferOutput 
> /autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
> Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 
> x86_64 x86_64 x86_64 GNU/Linux
> 
> recon-all -s  exited with ERRORS at Mon Jan 19 22:27:18 EST 2015
> 
> For more details, see the log file 
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> 
> Thanks so much, 
> Mia 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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> 
> 

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[Freesurfer] using merge_stats_tables to merge broadman areas for multiple subjects.

[Salil Soman]

Hi,

Following earlier device from this list, I was able to run the
merge_stats_tables command for a single subject as so:

merge_stats_tables --inputs $SUBJECTS_DIR/SUBJ_ID1/stats/lh.BA.stats
--all-segs --tablefile test_lh_BA_Stats_volumes.txt --meas volume

But when I tried to pass a series of subjects:

merge_stats_tables --inputs $SUBJECTS_DIR/SUBJ_ID1/stats/lh.BA.stats
$SUBJECTS_DIR/SUBJ_ID2/stats/lh.BA.stats --all-segs --tablefile
test_lh_BA_Stats_volumes.txt --meas volume

I get the error "duplicate row found: BA1, not sure if identical data,
therefore stopping!"

Is there a way to use merge_stats_tables to combine the broadman area
volumes for multiple subjects into 1 table?

Thanks!

-Sal
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[Freesurfer] converting .nii to .mgz

[Borzello, Mia]

Hi Freesurfers, 

I'm looking at Freesurfer files from are from years ago trying to look at the 
ct.anat file. Unfortunately, i have the nifti file and not the mgz file, so I'm 
wondering if there is a way to create it. In trying to find an answer online, I 
found this: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013493.html
I tried that but got an error. It may be a syntax error; this was my command 
line: recon-all -i 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii 
MG17_SurferOutput 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/


FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

  machine: huygens

  SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

  PWD: /autofs/space/huygens_001/users/mia/subjects

  ssh huygens
  setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
  cd /autofs/space/huygens_001/users/mia/subjects


1) MG17
2) recon-all -i 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii 
MG17_SurferOutput 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
3) ERROR: Flag 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii 
unrecognized.
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/ct.anat.nii 
MG17_SurferOutput 
/autofs/space/huygens_001/users/mia/subjects/MG17_SurferOutput/mri/
Linux huygens 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s  exited with ERRORS at Mon Jan 19 22:27:18 EST 2015

For more details, see the log file 
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Thanks so much, 
Mia 
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Re: [Freesurfer] regarding license.txt file

[zkaufman]

The freesurfer installation does NOT contain a license file. You must
create it, first by creating a file called license.txt in your
FREESURFER_HOME directory, then copy/paste the contents specified in the
email you recieved into the license.txt file.

-Zeke


> Hi,
>
> I downloaded the latest version of the freesurfer and tried to install it.
> After running the installation, I registered my information in
> https://surfer.nmr.mgh.harvard.edu/registration.html
>
> I received an email after few minutes with an information that I have to
> replace a text inside the license.txt file. So, I went back and try to do
> that. But I cannot locate the license.txt file. It does contain LICENSE
> file but doesn't have an information that I need to replace.
>
> Later, I went back and download the latest version of freesurfer again
> thinking I may have made a mistake at first installation but even the
> later installation didn't contain any license.txt file.
>
> The freesurfer that I download was from
> https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#Download
>
> The detail of the file is below
> Linux
>
> CentOS 6 x86_64 (64b)
>
> stable v5.3.0
>
> 15 May 2013
>
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>
> 4.2G
>
>
> Thank you for you time.
>
> Regards,
>
> Prabesh?
>
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[Freesurfer] regarding license.txt file

[Kanel, Prabesh]

Hi,

I downloaded the latest version of the freesurfer and tried to install it. 
After running the installation, I registered my information in 
https://surfer.nmr.mgh.harvard.edu/registration.html

I received an email after few minutes with an information that I have to 
replace a text inside the license.txt file. So, I went back and try to do that. 
But I cannot locate the license.txt file. It does contain LICENSE file but 
doesn't have an information that I need to replace.

Later, I went back and download the latest version of freesurfer again thinking 
I may have made a mistake at first installation but even the later installation 
didn't contain any license.txt file.

The freesurfer that I download was from 
https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall#Download

The detail of the file is below
Linux

CentOS 6 x86_64 (64b)

stable v5.3.0

15 May 2013

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

4.2G


Thank you for you time.

Regards,

Prabesh?

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Re: [Freesurfer] Creating a .gca file

[Bruce Fischl]

Hi Pradeep

pbsubmit is a wrapper script for submitting a job to a PBS cluster. If you 
don't have a cluster you should just run the commands that it runs.

cheers
Bruce



On Mon, 19 Jan 2015, pradeep mahato wrote:

> Hello experts,
> I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I am trying to
> create a atlas using previous registered subjects.
> It does not complete the mri_ca_normalize phase and stops there. It shows
> pbsubmit: Command not found as error.
> 
> Please correct me. Also attaching the rebuild_gca_atlas file.
> 
> Thanks
> 
> Pradeep Kumar Mahato
> 
>
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[Freesurfer] using -cw256 as default is good?

[Daniel Ferreira]

Dear experts,

We are processing a dataset that gives us this error  quite often:

ERROR! FOV=300.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.

Is it ok if I use -cw256 by default to all my scans even for those with
FOV=256 that do not need such flag?

Thanks

Best regards

Dani
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[Freesurfer] Confirm Siemens 3T Trio sequence parameters please

[Jason Steffener]

Could someone please confirm that the following parameters will result
in optimized data for grey matter volumetry with Freesurfer.
If there are changes that would be better I would really appreciate
that as well.

Siemens MPRAGE (Magnetization Prepared RApid Gradient Echo)
9 minutes and 50 seconds.
TI = 900 ms
TR = 2300 ms
TE = 4.18 ms
flip angle = 9 degrees
1mm isotropic voxels
256mm field-of-view
256 x 256 image matrix


Thank you,
Jason
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[Freesurfer] Creating a .gca file

[pradeep mahato]

Hello experts,
I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I am trying to
create a atlas using previous registered subjects.
It does not complete the mri_ca_normalize phase and stops there. It shows
pbsubmit: Command not found as error.

Please correct me. Also attaching the rebuild_gca_atlas file.

Thanks

Pradeep Kumar Mahato


rebuild_gca_atlas.csh
Description: C-Shell script
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