Hi,
I was trying to install Freesurfer on a HPC cluster. It seems to be a pretty large distribution, ~4.3 GB after unpacking. I wonder if all the subfolders are needed for running freesurfer or is there any folders could be skipped. Thanks in advance.
DJ
DJ,
Agreed that the distribution has gotten bloated. In future releases I'd like to change it to not include most of the data and to have recon-all or other utilities print a 'wget' command to use to download the data when needed.
I've updated the ReleaseNotes section with a list of some directories of stuff that is not used in the default stream. So deletion depends on whether you or your local user-base will ever need these, which can be tough to predict:
* freesurfer/average/mult-comp-cor - Correction for Multiple Comparisons pre-calc - 1.3G * freesurfer/subjects/fsaverage? - fsaverage at other iso-levels - 310M * freesurfer/subjects/fsaverage_sym - symmetric fsaverage for contra-lateral surface mapping - 197M * freesurfer/subjects/cvs_avg* - CVS Combined Volume and Surface registration target - 531M * freesurfer/trctrain - Tracula training set - 886M
These files in total are about 3GB.
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
Nick
On Tue, 2013-03-05 at 13:43 -0600, Dian Jiao wrote:
Hi,
I was trying to install Freesurfer on a HPC cluster. It seems to be a pretty large distribution, ~4.3 GB after unpacking. I wonder if all the subfolders are needed for running freesurfer or is there any folders could be skipped. Thanks in advance.
DJ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the info, Nick. That is very helpful.
Our install partition has limited size. So the idea is not to get rid of anything, but rather move these big data files somewhere else with much larger disk quota. I guess I could move the whole subject away. As long as SUBJECTS_DIR is set correctly, it should look at the right place when needed. However, can the same method applied to other big directories, e.g. average, lib? I don't see any corresponding environment variables.
Please advice.
On Tue, Mar 5, 2013 at 4:54 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
DJ,
Agreed that the distribution has gotten bloated. In future releases I'd like to change it to not include most of the data and to have recon-all or other utilities print a 'wget' command to use to download the data when needed.
I've updated the ReleaseNotes section with a list of some directories of stuff that is not used in the default stream. So deletion depends on whether you or your local user-base will ever need these, which can be tough to predict:
- freesurfer/average/mult-comp-cor - Correction for Multiple Comparisons pre-calc - 1.3G
- freesurfer/subjects/fsaverage? - fsaverage at other iso-levels - 310M
- freesurfer/subjects/fsaverage_sym - symmetric fsaverage for contra-lateral surface mapping - 197M
- freesurfer/subjects/cvs_avg* - CVS Combined Volume and Surface registration target - 531M
- freesurfer/trctrain - Tracula training set - 886M
These files in total are about 3GB.
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
Nick
On Tue, 2013-03-05 at 13:43 -0600, Dian Jiao wrote:
Hi,
I was trying to install Freesurfer on a HPC cluster. It seems to be a pretty large distribution, ~4.3 GB after unpacking. I wonder if all the subfolders are needed for running freesurfer or is there any folders could be skipped. Thanks in advance.
DJ _______________________________________________ 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.
DJ,
symbolic links would work. for instance:
cd freesurfer mv average <path_to_larg_disk_space>/freesurfer_data ln -s <path_to_larg_disk_space>/freesurfer_data/average
then you should have a link to average remaining in the freesurfer dir but the space is consumed elsewhere.
Nick
On Wed, 2013-03-06 at 10:33 -0600, Dian Jiao wrote:
Thanks for the info, Nick. That is very helpful.
Our install partition has limited size. So the idea is not to get rid of anything, but rather move these big data files somewhere else with much larger disk quota. I guess I could move the whole subject away. As long as SUBJECTS_DIR is set correctly, it should look at the right place when needed. However, can the same method applied to other big directories, e.g. average, lib? I don't see any corresponding environment variables.
Please advice.
On Tue, Mar 5, 2013 at 4:54 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: DJ,
Agreed that the distribution has gotten bloated. In future releases I'd like to change it to not include most of the data and to have recon-all or other utilities print a 'wget' command to use to download the data when needed. I've updated the ReleaseNotes section with a list of some directories of stuff that is not used in the default stream. So deletion depends on whether you or your local user-base will ever need these, which can be tough to predict: * freesurfer/average/mult-comp-cor - Correction for Multiple Comparisons pre-calc - 1.3G * freesurfer/subjects/fsaverage? - fsaverage at other iso-levels - 310M * freesurfer/subjects/fsaverage_sym - symmetric fsaverage for contra-lateral surface mapping - 197M * freesurfer/subjects/cvs_avg* - CVS Combined Volume and Surface registration target - 531M * freesurfer/trctrain - Tracula training set - 886M These files in total are about 3GB. https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Nick On Tue, 2013-03-05 at 13:43 -0600, Dian Jiao wrote: > Hi, > > > I was trying to install Freesurfer on a HPC cluster. It seems to be a > pretty large distribution, ~4.3 GB after unpacking. I wonder if all > the subfolders are needed for running freesurfer or is there any > folders could be skipped. Thanks in advance. > > > DJ > _______________________________________________ > 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
-
Dian Jiao -
Nick Schmansky