Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that?
I've tried using the following command lines
cd /home/john/Anu (where I kept all the .nii files)
for x in * do
recon-all -i SZ*.nii -s $x -all done
But this is not working
Hi Anupa
in general recon-all only processes a single dataset at a time. You can run multiple versions of recon-all if you have the processors and memory to support it. Something like:
foreach x ( *) recon-all -i SZ.${x}.nii -s $x -all & end
assuming that you had already converted your dicom files to nifti and named them accordingly.
You will need 4G of ram and a cpu for each process to make this worthwhile I think
cheers Bruce
On Sat, 7 Sep 2013, Anupa AV wrote:
Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that?
I've tried using the following command lines
cd /home/john/Anu (where I kept all the .nii files)
for x in * do recon-all -i SZ*.nii -s $x -all done
But this is not working
The problem here is that SZ*.nii presumably refers to a list of files due to shell expansion. I don't know how recon-all handles that (e.g. if it will take only the first file in the list, or all files), but that command probably won't do what you want it to.
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anupa AV [av.anupa@yahoo.com] Sent: Saturday, September 07, 2013 5:56 AM To: KOOL; Freesurfer Subject: [Freesurfer] recon-all for multiple subjects
Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that?
I've tried using the following command lines
cd /home/john/Anu (where I kept all the .nii files)
for x in * do recon-all -i SZ*.nii -s $x -all done
But this is not working
it won't handle it. If you gave it multiple inputs each with it's own -i it would assume that they are different images of the same subject and perform motion correction and averaging. I don't think that is the case here - you want to give each instance of recon-all a single nifti volume as input (unless you acquired multiple T1-weighted images/session)
cheers Bruce
On Sat, 7 Sep 2013, Watson, Christopher wrote:
The problem here is that SZ*.nii presumably refers to a list of files due to shell expansion. I don't know how recon-all handles that (e.g. if it will take only the first file in the list, or all files), but that command probably won't do what you want it to.
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anupa AV [av.anupa@yahoo.com] Sent: Saturday, September 07, 2013 5:56 AM To: KOOL; Freesurfer Subject: [Freesurfer] recon-all for multiple subjects
Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that?
I've tried using the following command lines
cd /home/john/Anu (where I kept all the .nii files)
for x in * do recon-all -i SZ*.nii -s $x -all done
But this is not working
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Anupa, If you want to run several subjects at the same time just open different command windows. On each you can run a recon all. You can also run a list of recon on each window. Just put the commands in a text file, name it something like i.e. group1.sh and run the command "sh group1.sh". Each subject will be done in sequence and each command window can have its own sequence. If you add the appropriate linux command you can also receive an email when the list of subjects is done.
Hope helps
2013/9/7 Bruce Fischl fischl@nmr.mgh.harvard.edu
it won't handle it. If you gave it multiple inputs each with it's own -i it would assume that they are different images of the same subject and perform motion correction and averaging. I don't think that is the case here - you want to give each instance of recon-all a single nifti volume as input (unless you acquired multiple T1-weighted images/session)
cheers Bruce
On Sat, 7 Sep 2013, Watson, Christopher wrote:
The problem here is that SZ*.nii presumably refers to a list of files
due to shell expansion. I don't know how recon-all handles that (e.g. if it will take only the first file in the list, or all files), but that command probably won't do what you want it to.
From: freesurfer-bounces@nmr.mgh.harvard.edu [
freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anupa AV [ av.anupa@yahoo.com]
Sent: Saturday, September 07, 2013 5:56 AM To: KOOL; Freesurfer Subject: [Freesurfer] recon-all for multiple subjects
Dear Sir, I'd like to know the command lines for running recon-all for multiple
datasets.
Can you please help me on that?
I've tried using the following command lines
cd /home/john/Anu (where I kept all the .nii files)
for x in * do recon-all -i SZ*.nii -s $x -all done
But this is not working
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Dear All, This worked for me... for x in SZ1 SZ2 SZ3 do recon-all -i $x.nii -s $x -all -hippo-subfileds done
Thanks for your valuable inputs...
________________________________ From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: "Watson, Christopher" Christopher.Watson@childrens.harvard.edu Cc: Anupa AV av.anupa@yahoo.com; KOOL P.C.M.P.Koolschijn@uva.nl; Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, September 7, 2013 7:10 PM Subject: Re: [Freesurfer] recon-all for multiple subjects
it won't handle it. If you gave it multiple inputs each with it's own -i it would assume that they are different images of the same subject and perform motion correction and averaging. I don't think that is the case here - you want to give each instance of recon-all a single nifti volume as input (unless you acquired multiple T1-weighted images/session)
cheers Bruce
On Sat, 7 Sep 2013, Watson, Christopher wrote:
The problem here is that SZ*.nii presumably refers to a list of files due to shell expansion. I don't know how recon-all handles that (e.g. if it will take only the first file in the list, or all files), but that command probably won't do what you want it to.
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anupa AV [av.anupa@yahoo.com] Sent: Saturday, September 07, 2013 5:56 AM To: KOOL; Freesurfer Subject: [Freesurfer] recon-all for multiple subjects
Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that?
I've tried using the following command lines
cd /home/john/Anu (where I kept all the .nii files)
for x in * do recon-all -i SZ*.nii -s $x -all done
But this is not working
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@nmr.mgh.harvard.edu
-
Anupa AV -
Bruce Fischl -
Dorian P. -
Watson, Christopher