Hi! Thank you for quick response! Yes, Pat1 and Pat2, etc are already imported into the freesurfer directory. So what I want to do do the further processing. Sorry, but I'm kind of confuse, I following the online tutorials:
(1) recon-all -s Pat1 \ -i <path_to_dicoms>/95555-2-1.dcm recon-all -s Pat2 \ -i <path_to_dicoms>/95555-2-1.dcm and so on.... (2) recon-all -s <subjid> -all Part (1) is completed for all my patients and I would like to do part (2) for all my patients at the same time. Isn't the right way to procede by typing in the terminal as below? recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -i -all Once again thank you for all your help! Best regards; Cecilio. 2015-04-30 22:35 GMT+08:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > Hi Cecilio > > are Pat1 and Pat2 etc... different patients? If so, they need to be run > separately. e.g. > > recon-all -s Pat1 -i <path to dicoms for patient 1) -all > recon-all -s Pat2 -i <path to dicoms for patient 2) -all > . > . > . > > cheers > Bruce > > p.s. for the tcsh bug you should just get your sysadmin to update the > version of tcsh you are using. > > On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: > > Dear professor Bruce! >> >> Sorry for bothering again, well I did exatly as you told before in order >> to >> process different subject at the same time: >> >> recon-all -s Pat1 -i Pat2 -i Pat3 -i Pat5 -all >> >> there Pat 1 (and the rest) are subjid. thought I got this error message: >> >> ARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! >> >> ERROR: cannot find Pat2 >> Linux cecilio-N73SV 3.8.0-44-generic #66~precise1-Ubuntu SMP Tue Jul 15 >> 04:01:04 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s Pat1 exited with ERRORS at Thu Apr 30 22:17:19 CST 2015 >> >> For more details, see the log file >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> Could that be an bug in the program? >> >> Once again! Thank you for your help! >> >> Best regards; Cecilio. >> >> >> 2015-04-29 1:09 GMT+08:00 Cecilio C Baro Perez <cecilio.c.b...@gmail.com >> >: >> 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. > >
_______________________________________________ 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.
