Hi again, - Yes, if you want the whole hippocampal volumes, you can just add all the substructures. - If you compare such volumes with those from aseg.stats, you'll see that they are 10%-15% smaller, but very highly correlated. We have observed that the addition of the 5.3 subfields is a tiny bit better when it comes to separating AD from controls based solely on hippocampal volume, though. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Cecilio C Baro Perez" <cecilio.c.b...@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, May 21, 2015 11:03:04 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hola Eugenio! Thank you so much for quick answer. Well telling from your response it seems that the right way to proceed in order to achieve the absolute volume is to sum up "ALL" given regions right? And could you please also tell me, which of the hippocampal volumes is the most correct one, the one given primarily by the "recon-all" or the "segmented" one? Thank you in advance! Best regards; Cecilio. 2015-05-21 16:54 GMT+08:00 Eugenio Iglesias < e.igles...@bcbl.eu > : Hola Cecilio, Right-Hippocampus and Left-Hippocampus are generic labels for the hippocampal regions that were not labeled as subiculum, CA, or fimbria in the atlas. In practice, they correspond to the hippocampal tails. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Cecilio C Baro Perez" < cecilio.c.b...@gmail.com > To: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > Sent: Thursday, May 21, 2015 4:35:31 AM Subject: Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3 Hi professor Bruce! I got finally the segmentation of the hippocampus I was looking for. Thought I have one more question I hope ypou could answer: By using : "kvlQuantifyPosteriorProbabilityImages $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ ? posterior_right_* posterior_Right-Hippocampus.mgz" I got the the fallowing answer: right_CA1: 2499.75 right_CA2_3: 7372.95 right_CA4_DG: 4296.22 right_fimbria: 665.066 right_hippocampal_fissure: 390.295 right_presubiculum: 3844.54 right_subiculum: 4969.41 Right-Hippocampus: 2709.7 I supposed the the total hippocampal quantification was done by summing those up and multiplying it by 0,5^3 . But what is the last subfield (the one by the name Right_Hippocampus)? Should I include it in the sum or is it already the final Right hippocampus in mm3? Once again thank you so much for all your help! Best regards; Cecilio. 2015-05-14 20:47 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu > : Hi Cecilio all our measures are in native space and not corrected for head size. The estimated total intracranial volume (etiv) is what we typically use for correction, and it should be in the aseg.stats file. In general I think it is preferable to use it as a regressor rather than divide, but perhaps someone can comment on this. We also segment the whole hippocampus, and which one you use is up to you (you could add up all the subfield volumes, but you won't get the same volume as the hippocampus from the aseg as the definitions are a bit different as are the algorithms). cheers Bruce On Thu, 14 May 2015, Cecilio C Baro Perez wrote: Dear professor Bruce! Sorry for bothering you again! I'm about to extract the hippocampus volume of a group of FS processed patients. Though, I have a few questions without explicit answers on the Internet. As recommended on FS tutorials I'm using this commando on the terminal: "recon-all -s xxxx -hippo-subfields". But will the hippocampus quantified be corrected for headsize or do I need to separately divide it with the total head-size? In the case of yes, could you please tell me where the total head volume could be found? I saw that the command "less aseg.stats" gives the hippocampal volume as well, in that case what is the reason of performing point 1 (above)? Thank you in advance! Best regards; Cecilio. 2015-05-01 0:06 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu >: Hi Cecilio you need more computers, or run it on the amazon cloud. Pedro Paulo has some utilities for this cheers Bruce On Fri, 1 May 2015, Cecilio C Baro Perez wrote: Oh thank you, that makes things much more clear! So prefessor, that means that there is any way possible to speed up the freesurfer processing? I have 30 patients and for each of the it takes like 25 h. Best regards; Cecilio. 2015-04-30 23:33 GMT+08:00 Bruce Fischl < fis...@nmr.mgh.harvard.edu >: no, you need to run each subject separately. What I was saying is that you don't need to separate out the importing into two steps. You can run: recon-all -s Pat1 \ -i <path_to_dicoms>/95555-2-1.dcm \ -all for each subject cheers Bruce On Thu, 30 Apr 2015, Cecilio C Baro Perez wrote: 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) fo r all my patients at the same time. Isn't the right way to procede by typing i n 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. _______________________________________________ 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 _______________________________________________ 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
