Thank you so much for your quick and helpful response! Best regards, Cecilio.
2015-04-26 20:27 GMT+08:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > sorry Cecilio, it is pretty compute intensive. If you have multiple cores > you can use -openmp to speed things up a bit, or just run more than one > recon-all at a time. Note that you don't need to invoke it twice - just run: > > recon-all -s ----- -i --- -all > > cheers > Bruce > > > > On Sun, 26 Apr 2015, Cecilio C Baro Perez wrote: > > Dear professor Bruce! >> >> Thank you so much for your help, it help me a lot! I have a silly >> question, >> sorry for that, I'm using the Freesurfer to extract the hippocampal volume >> of two different groups. Right using this two commands: >> >> "recon-all -s ----- -i followed by"recon-all -s ------all" >> >> Is taking like a day of processing for just one patient. Is there any >> faster >> way as I'm only interested on the hippocampal volume? >> >> Once again thank you for your help! >> >> Best regards; Cecilio. >> >> 2015-04-25 22:10 GMT+08:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> Hi Cecilio >> >> what do you mean "224 scans"? I assume you mean 224 slices in >> each scan? And do you have two different runs of the same scan >> type (e.g. mprage) for each subject? You can try: >> >> mri_info /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >> >> and >> >> freeview /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >> >> to find out the scan parameters and also visualize it. >> >> cheers >> Bruce >> >> >> On Sat, 25 Apr 2015, Cecilio C Baro Perez wrote: >> >> Hi Bruce! >> Thank you for your quick replay! I appreciate that! >> Well my data is T1 dicom >> images. And For every subject I have 224 scans. >> Though as I'm using >> freesurfer I'm trying by only using 2 of 224 scans. >> Please correct me if I'm >> wrong: >> File name: Pat1 >> Number of scans in Pat1: 2 (81334010 and 81334011) >> >> On terminal: >> Input command: >> 1. recon-all -s Patient1 -i >> /home/cecilio/Desktop/freesurfer/Test/Pat1/81334010 >> (this is executed free >> from errors) >> 2. recon-all -s Patient1 -all >> My error becomes: >> #@# Talairach Failure Detection Сб. апр. 25 18:25:07 >> CST 2015 >> >> recon-all -s Patient1 exited with ERRORS at Сб. апр. >> 25 18:25:32 CST 2015 >> >> Besides if I try to use the tkmedit I get this >> following: >> Tkmedit couldn't read the volume you specified. >> This could be because the image format wasn't >> recognized, >> or it couldn't find the proper header, >> or the file(s) were unreadable, >> or it was the wrong size. >> >> >> Please do you possibly know how to go around this >> problem. >> >> Thank you in advance! >> >> >> Best regards; Cecilio. >> >> 2015-04-24 21:20 GMT+08:00 Bruce Fischl >> <fis...@nmr.mgh.harvard.edu>: >> Hi Cecilio >> >> this means that the automatic checking >> determined that the >> Talairach transform to be very unlikely and >> probably a failure. >> What was your input data? If you bring it up >> in tkmedit or >> freeview do the directions on the screen >> correspond to true >> anatomical ones (e.g. is A really anterior)? >> >> cheers >> Bruce >> >> >> On Fri, 24 Apr 2015, Cecilio C Baro Perez >> wrote: >> >> >> >> >> Hi! >> My name is Cecilio! I'm using the >> freesurfer 5.3 and >> I'm having some issues >> that I hope you could help me with. When >> I perform: >> >> recon-all -s patienttesta -all >> >> I get this error: >> recon-all -s patienttesta exited with >> ERRORS >> ERROR: talairach_afd: Talairach >> Transform: >> transforms/talairach.xfm >> >> After reading on the internet I even try >> this >> command: >> recon-all -s patienttesta -all >> -use-mritotal >> >> But it stills give me the same error >> >> >> Could you please tell me what the >> problem could be? >> >> Thank you in advance! >> >> Best regards, Cecilio. >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> > _______________________________________________ > 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.
