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. > >
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