Dear Douglas,
It's an anatomical analysis. Perhaps I misunderstood the requirement for setting up the directories in the FSFAST for the recon-all command.
If that is the case, it is then a matter of converting my img files into mgz and run recon-all on them, am I right?
Does the command recon-all also gives me volumes for specific Brodmann's areas? Or do I have to run a labeling to that?
Thank you,
luis
If you're doing anatomical analysis, then FSFAST is not needed (nor its directly structure). If you have an input anatomical volume in any format, then just run
recon-all -s yoursubjectname -all -i inputfile
inputfile can include img but be warned that img does not have information about head orientation. This may cause a catastrophic failure (eg, the head is upside down). If the head is left-right reversed, then it probably won't fail but everything will be left-right reversed. don't say I did not warn you:)
On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo wrote:
Dear Douglas,
It's an anatomical analysis. Perhaps I misunderstood the requirement for setting up the directories in the FSFAST for the recon-all command.
If that is the case, it is then a matter of converting my img files into mgz and run recon-all on them, am I right?
Does the command recon-all also gives me volumes for specific Brodmann's areas? Or do I have to run a labeling to that?
Thank you,
luis
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Do I have to run recon-all entirely in order to extract volume for a few Brodmann's areas? Or is there a way of optimizing the process by striping it of any unneeded calculations?
It is taking 21h to analyze one subject.
Best, luis
2015-12-22 9:44 GMT+11:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
If you're doing anatomical analysis, then FSFAST is not needed (nor its directly structure). If you have an input anatomical volume in any format, then just run
recon-all -s yoursubjectname -all -i inputfile
inputfile can include img but be warned that img does not have information about head orientation. This may cause a catastrophic failure (eg, the head is upside down). If the head is left-right reversed, then it probably won't fail but everything will be left-right reversed. don't say I did not warn you:)
On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo wrote:
Dear Douglas,
It's an anatomical analysis. Perhaps I misunderstood the requirement for setting up the directories in the FSFAST for the recon-all command.
If that is the case, it is then a matter of converting my img files into mgz and run recon-all on them, am I right?
Does the command recon-all also gives me volumes for specific Brodmann's areas? Or do I have to run a labeling to that?
Thank you,
luis
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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you have to do the whole thing
On 12/21/2015 06:09 PM, Luis Fernado Silva Castro de Araújo wrote:
Do I have to run recon-all entirely in order to extract volume for a few Brodmann's areas? Or is there a way of optimizing the process by striping it of any unneeded calculations?
It is taking 21h to analyze one subject.
Best, luis
2015-12-22 9:44 GMT+11:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
If you're doing anatomical analysis, then FSFAST is not needed (nor its directly structure). If you have an input anatomical volume in any format, then just run recon-all -s yoursubjectname -all -i inputfile inputfile can include img but be warned that img does not have information about head orientation. This may cause a catastrophic failure (eg, the head is upside down). If the head is left-right reversed, then it probably won't fail but everything will be left-right reversed. don't say I did not warn you:) On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo wrote: > > Dear Douglas, > > It's an anatomical analysis. Perhaps I misunderstood the requirement > for setting up the directories in the FSFAST for the recon-all command. > > If that is the case, it is then a matter of converting my img files > into mgz and run recon-all on them, am I right? > > Does the command recon-all also gives me volumes for specific > Brodmann's areas? Or do I have to run a labeling to that? > > > Thank you, > > luis > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Hi Luis
sorry, the BA stuff is almost at the very end so you will need to run pretty much everything. We are down to 8 hours or so on modern multi-core CPUs (and even faster than that with 4-8 threads)
cheers Bruce On Tue, 22 Dec 2015, Luis Fernado Silva Castro de Araújo wrote:
Do I have to run recon-all entirely in order to extract volume for a few Brodmann's areas? Or is there a way of optimizing the process by striping it of any unneeded calculations?
It is taking 21h to analyze one subject.
Best, luis
2015-12-22 9:44 GMT+11:00 Douglas N Greve greve@nmr.mgh.harvard.edu: If you're doing anatomical analysis, then FSFAST is not needed (nor its directly structure). If you have an input anatomical volume in any format, then just run
recon-all -s yoursubjectname -all -i inputfile inputfile can include img but be warned that img does not have information about head orientation. This may cause a catastrophic failure (eg, the head is upside down). If the head is left-right reversed, then it probably won't fail but everything will be left-right reversed. don't say I did not warn you:) On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo wrote: > > Dear Douglas, > > It's an anatomical analysis. Perhaps I misunderstood the requirement > for setting up the directories in the FSFAST for the recon-all command. > > If that is the case, it is then a matter of converting my img files > into mgz and run recon-all on them, am I right? > > Does the command recon-all also gives me volumes for specific > Brodmann's areas? Or do I have to run a labeling to that? > > > Thank you, > > luis > > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
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Bruce Fischl -
Douglas N Greve -
Luis Fernado Silva Castro de Araújo