Re: [Freesurfer] TRACULA statistics concern
Ciao Stefano, can you be a bit more specific about what you're exactly trying to to? Am I correctly assuming that you are looking at differences between your groups? Are you looking at average FA/MD/RD/AD over whole tracts, or at values along them? Do you have any strong hypothesis on which tract will give you differences? In any case, people often look at the tracts of interest one by one (which a simple test, e.g., t-test) and then apply Bonferroni correction. Kind regards, /Eugenio On Mon, 2014-03-24 at 21:39 +0100, std...@virgilio.it wrote: Hi list, I'm performing TRACULA on three groups for all 18 tracts and for FA, MD, RD, AD. Which is the best way to perform statistic on TRACULA outcomes? I think that MANCOVA is too hard and it delete interesting and consolidate (in literature) results. Thanks, Stefano ___ 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.
Re: [Freesurfer] R: Re: TRACULA statistics concern
Hi again, if you perform the same analysis over and over for each of the 18 tracts, then the Bonferroni corrected p-value would be 0.05/18 Cheers, /Eugenio On Mon, 2014-03-24 at 22:47 +0100, std...@virgilio.it wrote: Ciao Eugenio, thank you very much for your prompt and kind response. Yes, I'm looking average over the entire support of the path distribution and their differences among 2 pathological and 1 control groups. I haven't a strong hypothesis. When I performed MANOVA, Tukey or Bonferroni post hoc find differences but p for Wilk's lambda is not significant. If I understand your suggestion, I should performed a simple t-test for each tract. Bur, for Bonferroni's correction, I should consider: A. 0.05/18 tracts X 3 groups (I suspected that it should be too hard) or B. 0.05/18 tracts or more simply C. 0.05/3 groups Thanks, Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 24-mar-2014 22.11 A: std...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] TRACULA statistics concern Ciao Stefano, can you be a bit more specific about what you're exactly trying to to? Am I correctly assuming that you are looking at differences between your groups? Are you looking at average FA/MD/RD/AD over whole tracts, or at values along them? Do you have any strong hypothesis on which tract will give you differences? In any case, people often look at the tracts of interest one by one (which a simple test, e.g., t-test) and then apply Bonferroni correction. Kind regards, /Eugenio On Mon, 2014-03-24 at 21:39 +0100, std...@virgilio.it wrote: Hi list, I'm performing TRACULA on three groups for all 18 tracts and for FA, MD, RD, AD. Which is the best way to perform statistic on TRACULA outcomes? I think that MANCOVA is too hard and it delete interesting and consolidate (in literature) results. Thanks, Stefano ___ 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
Re: [Freesurfer] R: Re: TRACULA statistics concern
Unless you're comparing groups in a pairwise manner, i.e., A vs B, B vs C, and A vs C. In that case, you would have 18 x 3 comparisons and the threshold for significance would be 0.05 / (18 x 3) Cheers, /Eugenio On Mon, 2014-03-24 at 17:50 -0400, Juan Eugenio Iglesias wrote: Hi again, if you perform the same analysis over and over for each of the 18 tracts, then the Bonferroni corrected p-value would be 0.05/18 Cheers, /Eugenio On Mon, 2014-03-24 at 22:47 +0100, std...@virgilio.it wrote: Ciao Eugenio, thank you very much for your prompt and kind response. Yes, I'm looking average over the entire support of the path distribution and their differences among 2 pathological and 1 control groups. I haven't a strong hypothesis. When I performed MANOVA, Tukey or Bonferroni post hoc find differences but p for Wilk's lambda is not significant. If I understand your suggestion, I should performed a simple t-test for each tract. Bur, for Bonferroni's correction, I should consider: A. 0.05/18 tracts X 3 groups (I suspected that it should be too hard) or B. 0.05/18 tracts or more simply C. 0.05/3 groups Thanks, Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 24-mar-2014 22.11 A: std...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] TRACULA statistics concern Ciao Stefano, can you be a bit more specific about what you're exactly trying to to? Am I correctly assuming that you are looking at differences between your groups? Are you looking at average FA/MD/RD/AD over whole tracts, or at values along them? Do you have any strong hypothesis on which tract will give you differences? In any case, people often look at the tracts of interest one by one (which a simple test, e.g., t-test) and then apply Bonferroni correction. Kind regards, /Eugenio On Mon, 2014-03-24 at 21:39 +0100, std...@virgilio.it wrote: Hi list, I'm performing TRACULA on three groups for all 18 tracts and for FA, MD, RD, AD. Which is the best way to perform statistic on TRACULA outcomes? I think that MANCOVA is too hard and it delete interesting and consolidate (in literature) results. Thanks, Stefano ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] hippocampal subfields
Dear Gabor, the segmentation benefits to some extent from higher resolution data, but produces decent estimates of the subfields at 1x1x1. We are working on a new atlas that will incorporate much more detail, and will more effectively take advantage of high-resolution images. Kind regards, Juan Eugenio Iglesias On Mon, 2014-03-03 at 13:49 +0100, Gabor Perlaki wrote: Dear all, 1. Which is the suggested resolution for hippocampal subfields segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields segmentation really work with 1.0*1.0*1.0 resolution? 2. The article Automated Segmentation of Hippocampal Subfields from Ultra-High Resolution In Vivo MRI. suggested on Freesurfer's page uses FOV=448. We are unable to set up the matrix to achieve 0.38mm resolution using this FOV. Is there any other suggested article to set up our measurements? Thanks, -- Gabor Perlaki ___ 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.
Re: [Freesurfer] Extracting only hippo campus volume
Hi Saurabh, the volume of the hippocampal subfields can be computed with: cd $SUBJECTS_DIR/bert/mri kvlQuantifyPosteriorProbabilityImages \ $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt \ posterior_right_* posterior_Right-Hippocampus.mgz and the whole hippocampal volume is just the aggregate. Note that 1: - this volume is no necessarily equal to that estimated from aseg.mgz. - this volume is in voxels defined at 0.5mm resolution, so you will need to divide it by 8 to translate them into cubic millimeters. To visualize aseg.mgz: did you change the color map to lookup table? Cheers, /Eugenio On Fri, 2014-02-28 at 12:41 -0500, Bruce Fischl wrote: Hi Saurabh I didn't realize you meant the subfields. For that you'll need Koen or Eugenio to answer. You are probably seeing the cc in freeview because that is the default slice it shows, but you should be able to scroll around and see other stuff cheers Bruce On Fri, 28 Feb 2014, Saurabh Thakur wrote: Thanks for such quick reply Bruce, I am saying i am using these file , referring to feesurfer website. cd $SUBJECTS_DIR/bert/mri freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt which contains nu.mgz, posterior_Left-Hippocampus.mgz ,posterior_Right-Hippocampus.mgz when i am using aseg.mgz i am seeing corpus collosum in free viewer, why is it so...? And I will try to use commands which u referred and get back to you. cheers Saurabh Thakur, On Fri, Feb 28, 2014 at 6:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Saurabh I'm not sure what you mean by the main volume, but the hippocampus is segmented in the aseg.mgz. You can extract it from there using mri_extract_label or mri_binarize --match cheers Bruce On Fri, 28 Feb 2014, Saurabh Thakur wrote: Hello Freesurfer expert, I have done Hippo campus segmentation using Freesurfer. Can u tell me how to extract the only Hippo campus volume from nu.mgz Why only nu.mgz is used for the main volume--is there some specific reason to use? Thanks in advance , Saurabh Thakur, 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
Re: [Freesurfer] Hippocampal Subfield Segmentation
Dear Sierra, there's no direct correspondence between these subfields and head / body. If you want, you could create a geometric rule to subdivide the hippocampus into head / body / tail, e.g., by creating a coordinate system based on the major axis of the hippocampal shape. Kind regards, Eugenio On Tue, 2014-01-14 at 18:07 +, Germeyan, Sierra (NIH/NINDS) [F] wrote: Hi everyone, In using Van Leemput's -hippo-subfields flag as part of the recon-all script to obtain hippocampal subfield volumes, my lab has determined that larger subfields are more relevant for our purposes clinically/surgically. Is there a way to group the fimbria/CA1/2,3/4,DG/presubiculum/subiculum/hippocampal fissure/etc. subfields such that they correspond to the head, body, and tail of the hippocampus? I am aware that the subfield hippocampus refers to part of the tail of the hippocampus, but beyond that, it is unclear how these subfields should be categorized. Thanks for the help! Sierra Germeyan, B.A. Clinical Epilepsy Section, NINDS, NIH ___ 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.
Re: [Freesurfer] longitudinal hippocampal subfields
Dear Joana, at this point, a true longitudinal version of the subfield segmentation is not available. However, we have noticed that you can get slightly better (more stable) results by segmenting the subfields in the longitudinally processed timepoints - rather than the original, cross-sectionally analyzed subjects that you used to create the base. In other words: rather than running recon-all -subjid tpN -hippo-subfields you should run recon-all -subjid tpN.long.base -hippo-subfields Cheers, Eugenio On 11/06/2013 11:32 AM, Joana Braga Pereira wrote: Dear all, I'm interested in assessing the changes in the volumes of hippocampal subfields between 2 time points. Can I use the longitudinal pipeline of Freesurfer and add the -hippo-subfields flag to the longitudinal runs of the 2 time points? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] -hippo-subfields error
Gari, can you send us the log of the hippo subfield module (or the screen output; they should be the same) Cheers, /Eugenio On 10/16/2013 10:22 AM, Garikoitz Lerma-Usabiaga wrote: Hi, I had a subject already run through recon-all. After making recon-all -s ID -hippo-subfields or recon-all -s ID -hippo-subfields -make all it is failing. It is the first subject ever failing with the hippo-subfields. The rest of the subjects are ok. This subject is properly segmented (tkmedit ID brainmask.mgz -surfs -aseg is ok). Any recommendations on what to do next? thanks! Gari PS1 please find attached the last recon-all invocation log. PS2 I have the screen output as well, there was more detail in that, in case it would help recognizing the problem. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] hippocampal subfield segmentations
Dear Gregory, we are indeed working on a new version, but we don't know when it will be available yet. Cheers, Eugenio On 10/04/2013 03:05 AM, Gregory Kirk wrote: I heard from Koen a while back that a new improved version was in the works. I have several projects I would be interested in using it for. Any info on timelines for release or a publication ? thank You ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Hippocampal subfield segmentation paused
Hi again, Irene, On 10/03/2013 09:39 AM, Irene Lee wrote: Hi, Eugenio, I have already sent the log files to you. Sorry, I should have been more specific. I meant [subject_dir]/scripts/recon-all.log and [subject_dir]/scripts/hippo-subfields.log And would you please give me a hint what is the right command for computing subfields with high-res T2? Thank you very much!! This is not an option at this point, but we are working on it. Cheers, /Eugenio -Irene *From:* Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu *To:* Irene Lee lee.iren...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, October 1, 2013 4:37 PM *Subject:* Re: [Freesurfer] Hippocampal subfield segmentation paused Hi Irene, two things: 1. Can you please send us the log files of the recon? 2. The command you executed will compute the subfield segmentation based only on the T1, not the high-res T2. Cheers, /Eugenio On 10/01/2013 04:30 PM, Irene Lee wrote: Hi, there, I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas. Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I used the command recon-all -s my subject -all -hippo-subfields It was running well, however, it halted/paused after it displayed the following information:final transformation (x=..,yr=..,zr=..) and a 4x4 matrix. For a week it is not going anywhere and not producing any output. The computer I was running it on had sufficient computational resources and a Fedora linux system. It does not seem to be related to the configuration of the computer. Has anyone ever encountered this problem?? Any diagnostic advice will be appreciated!! -Irene ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com http://www.jeiglesias.com/ igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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. -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Hippocampal subfield segmentation paused
Hi Irene, two things: 1. Can you please send us the log files of the recon? 2. The command you executed will compute the subfield segmentation based only on the T1, not the high-res T2. Cheers, /Eugenio On 10/01/2013 04:30 PM, Irene Lee wrote: Hi, there, I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas. Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I used the command recon-all -s my subject -all -hippo-subfields It was running well, however, it halted/paused after it displayed the following information:final transformation (x=..,yr=..,zr=..) and a 4x4 matrix. For a week it is not going anywhere and not producing any output. The computer I was running it on had sufficient computational resources and a Fedora linux system. It does not seem to be related to the configuration of the computer. Has anyone ever encountered this problem?? Any diagnostic advice will be appreciated!! -Irene ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Hippocampal Subfield Segmentation
Hi Sierra, the hippocampal subfield segmentation is computed using a separate model, so it doesn't agree perfectly with the hippocampal mask in aseg.mgz. In fact, the volume estimates tend to be a bit smaller (but highly correlated). Cheers, /Eugenio On 09/30/2013 10:42 AM, Germeyan, Sierra (NIH/NINDS) [F] wrote: Hi everyone, After running -hippo-subfields, I converted the voxel output of -hippo-subfields to mm^3 based on the instructions given here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/031188.html. Then I summed the volumes for all of the subfields (assuming that this would give me the total hippocampal volume), and compared the sum to the hippocampal volume that FreeSurfer gave after running recon-all -all on the same scan. They weren't the same! Why would these differ? Or, is there something I am doing wrong in my comparison of the two hippocampal outputs? Thanks for your help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] hippocampal subfields question
Hi Sal, yes, the label hippocampus corresponds to the tail. The units for the segmentation are voxels of the subfield segmentation. Since these voxels are cubes with a .5mm side, you need to divide the volumes by 8 to convert to cubic mm. Cheers, /Eugenio On 08/12/2013 09:13 PM, Salil Soman wrote: Hi, I just wanted to confirm that label hippocampus in the hippocampal subfields segmentation is simply parts of the hippocampus that do not fall into one of the other major categories? Also, where can I find the units for the hippocampal subfields? I am seeing some discrepancy between the left and right hippocampal volumes generated by freesurfer and the summed areas generated by the hippocampal subfield analysis. Thank you, -Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] hippo_subfields atlas
Hi again, Raja. Which labels and meshes to use depends on what you want to do. If you extract all the priors corresponding to all the labels in the atlas (the list is in $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt), you would have a volumetric version of the atlas (rather than a mesh). Cheers, /Eugenio On 08/07/2013 06:04 PM, Rajapillai Pillai wrote: Final question regarding this: what combinations of labels and meshes should I use? Should I do all combinations between labels and positions, matching labels/positions only, etc? How can I tell which meshes correspond to what labels/areas? Thanks for your time, Raja On Wed, Aug 7, 2013 at 4:26 PM, Rajapillai Pillai raja.i.pil...@gmail.com mailto:raja.i.pil...@gmail.com wrote: Thanks very much! On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Shame on me; there's a way of doing this. You need a reference volume; for the hippocampal subfield atlas: $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz the reference volume would be: $FREESURFER_HOME/data/GEMS/imageDump.mgz The command would be: kvlRasterizeAtlasMesh CurrentMeshCollection30.gz imageDump.mgz [labelNumber] [meshNumber] meshNumber is the index of the mesh to extract in the collection; use -1 for the reference position. labelNumber is the label whose probability map you want to rasterize ( 0 = white matter, 1 = gray matter, 2 = CSF, 9 = CA1, etc; see $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt). From the volumetric rasterized prior probability map, you can easily compute volumes, if you want. Cheers, and sorry again for the original wrong answer, /Eugenio On 08/07/2013 01:30 PM, Rajapillai Pillai wrote: Hi again! I have another question about the hippocampal subfields atlas--might be a silly one. Is there a way to extract volumes from the mesh collection? Thanks a lot, Raja On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Sounds good, but please email the list, rather than only me ;-) /E On 07/31/2013 05:03 PM, Rajapillai Pillai wrote: Thanks a lot. I'll let you know if I have any more issues. Best regards, Raja On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Did you run recon-all -subjid bert -hippo-subfields? If so, there should be a log file with the output from the hippo-subfield code in $SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it to get an idea of what happened. Kind regards, /Eugenio On 07/31/2013 04:38 PM, Rajapillai Pillai wrote: Thanks very much for the prompt response. The command I ran was $ kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz in $SUBJECTS_DIR/bert/mri And yeah, it's not in the mri directory. Any idea what might have gone wrong and how I can try and fix it? Thanks, Raja On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Hi Raja, I'm have a question regarding the GEMS hippocampal segmentation. I saw on the wiki how to run -hippo_subfields, but how do I access the atlas itself? What file is it under. That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz Also, I'm not sure if I'm missing some files: whenever I try to do one of the individual commands using, for example, posterior_Right_Hippocampus.mgz, it gives the following error: volumeInVoxels: terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: posterior_Right-Hippocampus.mgz Abort trap What
Re: [Freesurfer] hippo_subfields atlas
Shame on me; there's a way of doing this. You need a reference volume; for the hippocampal subfield atlas: $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz the reference volume would be: $FREESURFER_HOME/data/GEMS/imageDump.mgz The command would be: kvlRasterizeAtlasMesh CurrentMeshCollection30.gz imageDump.mgz [labelNumber] [meshNumber] meshNumber is the index of the mesh to extract in the collection; use -1 for the reference position. labelNumber is the label whose probability map you want to rasterize ( 0 = white matter, 1 = gray matter, 2 = CSF, 9 = CA1, etc; see $FREESURFER_HOME/data/GEMS/compressionLookupTable.txt). From the volumetric rasterized prior probability map, you can easily compute volumes, if you want. Cheers, and sorry again for the original wrong answer, /Eugenio On 08/07/2013 01:30 PM, Rajapillai Pillai wrote: Hi again! I have another question about the hippocampal subfields atlas--might be a silly one. Is there a way to extract volumes from the mesh collection? Thanks a lot, Raja On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Sounds good, but please email the list, rather than only me ;-) /E On 07/31/2013 05:03 PM, Rajapillai Pillai wrote: Thanks a lot. I'll let you know if I have any more issues. Best regards, Raja On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Did you run recon-all -subjid bert -hippo-subfields? If so, there should be a log file with the output from the hippo-subfield code in $SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it to get an idea of what happened. Kind regards, /Eugenio On 07/31/2013 04:38 PM, Rajapillai Pillai wrote: Thanks very much for the prompt response. The command I ran was $ kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz in $SUBJECTS_DIR/bert/mri And yeah, it's not in the mri directory. Any idea what might have gone wrong and how I can try and fix it? Thanks, Raja On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Hi Raja, I'm have a question regarding the GEMS hippocampal segmentation. I saw on the wiki how to run -hippo_subfields, but how do I access the atlas itself? What file is it under. That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz Also, I'm not sure if I'm missing some files: whenever I try to do one of the individual commands using, for example, posterior_Right_Hippocampus.mgz, it gives the following error: volumeInVoxels: terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: posterior_Right-Hippocampus.mgz Abort trap What command is this? In any case, it's pretty clear that the file is missing Also, upon searching through my freesurfer directory, I cannot find any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz files. It should be under the mri directory. If it isn't, there was some problem running the algorithms. Cheers, /Eugenio Thanks very much for your time, Raja ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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
Re: [Freesurfer] hippo_subfields atlas
Hi Raja, I'm have a question regarding the GEMS hippocampal segmentation. I saw on the wiki how to run -hippo_subfields, but how do I access the atlas itself? What file is it under. That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz Also, I'm not sure if I'm missing some files: whenever I try to do one of the individual commands using, for example, posterior_Right_Hippocampus.mgz, it gives the following error: volumeInVoxels: terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: posterior_Right-Hippocampus.mgz Abort trap What command is this? In any case, it's pretty clear that the file is missing Also, upon searching through my freesurfer directory, I cannot find any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz files. It should be under the mri directory. If it isn't, there was some problem running the algorithms. Cheers, /Eugenio Thanks very much for your time, Raja ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] hippo_subfields atlas
Did you run recon-all -subjid bert -hippo-subfields? If so, there should be a log file with the output from the hippo-subfield code in $SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it to get an idea of what happened. Kind regards, /Eugenio On 07/31/2013 04:38 PM, Rajapillai Pillai wrote: Thanks very much for the prompt response. The command I ran was $ kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_right_* posterior_Right-Hippocampus.mgz in $SUBJECTS_DIR/bert/mri And yeah, it's not in the mri directory. Any idea what might have gone wrong and how I can try and fix it? Thanks, Raja On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Hi Raja, I'm have a question regarding the GEMS hippocampal segmentation. I saw on the wiki how to run -hippo_subfields, but how do I access the atlas itself? What file is it under. That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz Also, I'm not sure if I'm missing some files: whenever I try to do one of the individual commands using, for example, posterior_Right_Hippocampus.mgz, it gives the following error: volumeInVoxels: terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: posterior_Right-Hippocampus.mgz Abort trap What command is this? In any case, it's pretty clear that the file is missing Also, upon searching through my freesurfer directory, I cannot find any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz files. It should be under the mri directory. If it isn't, there was some problem running the algorithms. Cheers, /Eugenio Thanks very much for your time, Raja ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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. -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files
Hi Jasmeet, what modification did you exactly make? Whih version of FreeSurfer is this? Cheers, /Eugenio On 07/17/2013 10:22 AM, Jasmeet Hayes wrote: Dear Freesurfer experts, I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two text files (left right stats) but the only information in the text files is the subject ID number. However, on my terminal window, I can see the volume output for each subfield and for each subject (see below for an example of 1 subject). And there were no errors after running the script. Every subject in the folder went through the hippocampal subfield recon procedure, and I have verified that there were no errors (each subject's folder has the left and right posterior_* files). We made a slight modification to the kvl script, only to change the Subject directory. Any ideas about what might be the problem? Thanks! -Jasmeet cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS IS THE COMPRESSION LOOKUP TABLE FILE /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before running KVLQuantifyPosteriorProb IS: /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 right_hippocampal_fissure: 541.872 cd .. cd .. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files
OK, then the question is why kvlQuantifyPosteriorProbabilityImages is producing an empty file I think the problem is that kvlQuantifyHippocampalSubfieldSegmentations.sh behaves in a different way depending on the number arguments, etc. I would suggest that you go back to the original version of the script, and use it the way it's described in http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation, that is, setting the environment variable SUBJECTS_DIR and calling the script without arguments. Kind regards, /Eugenio On 07/17/2013 11:46 AM, Jasmeet Hayes wrote: Hi Eugenio, We are using version 5.1. I attached our script. We added to line 60, setting the subject directory. We also changed the statFileName (see line 291 on the attached script). I should also note that the volumeStats_left and right text files within each subject's mri folder is empty. Thanks for your help. On Wed, Jul 17, 2013 at 11:16 AM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu wrote: Hi Jasmeet, what modification did you exactly make? Whih version of FreeSurfer is this? Cheers, /Eugenio On 07/17/2013 10:22 AM, Jasmeet Hayes wrote: Dear Freesurfer experts, I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two text files (left right stats) but the only information in the text files is the subject ID number. However, on my terminal window, I can see the volume output for each subfield and for each subject (see below for an example of 1 subject). And there were no errors after running the script. Every subject in the folder went through the hippocampal subfield recon procedure, and I have verified that there were no errors (each subject's folder has the left and right posterior_* files). We made a slight modification to the kvl script, only to change the Subject directory. Any ideas about what might be the problem? Thanks! -Jasmeet cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS IS THE COMPRESSION LOOKUP TABLE FILE /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before running KVLQuantifyPosteriorProb IS: /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 right_hippocampal_fissure: 541.872 cd .. cd .. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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. -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh
What was the exact call? Did you try setting SUBJECTS_DIR to the directory at hand and running the command without arguments? Cheers, /Eugenio On 06/25/2013 09:06 AM, Yang, Zoe wrote: Dear Eugenio, Thanks for the reply. Yes, we created a test directory containing two subjects that have been reconed with the --hippo-subfields flag. Both of them have 20 output files. Cheers, Zoe *From:*Juan Eugenio Iglesias [mailto:igles...@nmr.mgh.harvard.edu] *Sent:* Monday, June 24, 2013 5:03 PM *To:* Yang, Zoe *Cc:* 'Freesurfer@nmr.mgh.harvard.edu' *Subject:* Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh Dear Zoe, have you checked whether all directories within your subject directory correspond to subjects which have been reconed with the -hippo-subfields flag? Cheers, /Eugenio On 06/24/2013 04:00 PM, Yang, Zoe wrote: Hi all, I am getting error messages while running kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the error mentioned in an earlier email (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html). We did use the -hippo-subfields flag for all of our subjects first, and the output was 20 left and right subfield mgz files (it completed without any errors). The subjects had already undergone the standard volumetric FreeSurfer pipeline and therefore we ran the command: recon-all -s subjectID -hippo-subfields. The error message for kvlQuantifyHippocampalSubfieldSegmentation that I'm getting is: resultsDirectory ***/HIPPOCAMPAL_TEST cd ***/HIPPOCAMPAL_TEST resultsDirectory ***/HIPPOCAMPAL_TEST startIndex: 1 endIndex: 2 cd subjectID_recon/ Quantifying subject ID_recon left Doing left side cd left cd segmentationWithoutPartialVolumingLog kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x46b690): Can't find/open file: posterior_Left-Hippocampus.mgz kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 50779 Abort trap kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt Is there anything else that we are missing and should run? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu mailto:igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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 -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer
Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh
Hi again, Zoe, Marcos is right about the fact that the script fails if the posterior*.mgz are not found in any 1- Set your $SUBJECTS_DIR variable as another another path and move your subjects directories (and only these directories to this place) and run the same script you tried (kvlQuantifyHippocampalSubfieldSegmentations.sh) Rather than moving the subjects, I'd create symbolic links, but this is certainly an option. Another option is to modify kvlQuantifyHippocampalSubfieldSegmentations.sh, replacing the two instances of: doIt kvlQuantifyPosteriorProbabilityImages $compre. by cmd=kvlQuantifyPosteriorProbabilityImages $compre. eval $cmd Cheers, /Eugenio Em Seg, 2013-06-24 às 16:00 -0400, Yang, Zoe escreveu: Hi all, I am getting error messages while running kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the error mentioned in an earlier email (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html). We did use the -hippo-subfields flag for all of our subjects first, and the output was 20 left and right subfield mgz files (it completed without any errors). The subjects had already undergone the standard volumetric FreeSurfer pipeline and therefore we ran the command: recon-all -s subjectID -hippo-subfields. The error message for kvlQuantifyHippocampalSubfieldSegmentation that I’m getting is: resultsDirectory ***/HIPPOCAMPAL_TEST cd ***/HIPPOCAMPAL_TEST resultsDirectory ***/HIPPOCAMPAL_TEST startIndex: 1 endIndex: 2 cd subjectID_recon/ Quantifying subject ID_recon left Doing left side cd left cd segmentationWithoutPartialVolumingLog kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x46b690): Can't find/open file: posterior_Left-Hippocampus.mgz kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 50779 Abort trap kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt failed to do kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz volumeStats_left.txt Is there anything else that we are missing and should run? Thanks! ___ 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. -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Hippocampal subfields intensity
Dear Marcos,
these are just mean and standard deviations of intensities of the images
at different levels of processing. What the best measure is depends on
what you want to do with them.
Cheers,
/Eugenio
On Tue, 2013-06-11 at 11:46 -0300, Marcos Martins da Silva wrote:
Hi, Eugenio,
TY again for your help. I did the computing without errors after your
suggestions. I also computed the intensities based on nu.mgz, norm.mgz
and T1.mgz. I would like to know the best measure I should consider,
including because I intend to compare these values with intensity data
from basal ganglia and cortical areas as I can find in aseg.stats. It
follows my results:
norm.mgz based
meannorm= 78.725
variancenorm = 20.258(stdev = 4.50001)
nu.mgz based
meannu = 87.362
variancenu = 26.343 (stdev =5.132543229)
T1.mgz based
meant1 = 84.023
variancet1 = 23.277 (stdev =4.824624338)
It follows the MatLab/Octave code I used
Norm=MRIread('norm_postres.mgz');
datanorm=Norm.vol(:);
Ps=nMRIread('posterior_right_subiculum.mgz');
postsub=double(Ps.vol(:));
meannorm=sum(datanorm.*postsub)/sum(postsub);
variancenorm=sum((datanorm-meannorm).^2.*postsub)/sum(postsub);
Nu=MRIread('nu_postres.mgz');
datanu=Nu.vol(:);
meannu=sum(datanu.*postsub)/sum(postsub);
variancenu=sum((datanu-meannu).^2.*postsub)/sum(postsub);
T1=MRIread('T1_postres.mgz');
datat1=T1.vol(:);
meant1=sum(datat1.*postsub)/sum(postsub);
variancet1=sum((datat1-meant1).^2.*postsub)/sum(postsub);
The *postres.mgz files are nu, norm and T1 resampled as you suggested.
And nMRIread is the workarounded version of MRIread I said in previous
message.
Cheers,
Marcos
Em Seg, 2013-06-10 às 16:58 -0400, Juan Eugenio Iglesias escreveu:
Hi Marcos,
1. your fix of MRIread.m is great. I forgot of this bug; we should
totally take care of it.
2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
difference voxel space. So, you need to resample norm.mgz to the space
of the subfields. To do so, you can use mri_convert with the option -rl
(reslice like):
mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz
3. Now you can do:
A=MRIread('norm.mgz');
data=A.vol(:);
B=MRIread('posterior_subiculum.mgz');
post=double(B.vol(:));
mean=sum(data.*post)/sum(post);
variance=sum((data-mean).^2.*post)/sum(post);
Cheers,
/Eugenio
On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
Hi, Eugenio
TY for your fast help. I understood you were suggesting to compute
that on MatLab and I tried this:
NU=MRIread('nu.mgz')### that runs ok
Ps=MRIread('posterior_left_subiculum.mgz') ### it fails with the
following message
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bounds because
numel(mr_parms)=0.
Error in MRIread (line 100)
tr = mr_parms(1);
I solved creating a little customized nMRIread.m with the following
changes:
if numel(mr_parms) 0
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
else
mr_parms(1) = 0;
mr_parms(2) = 0;
mr_parms(3) = 0;
mr_parms(4) = 0;
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
end
With those changes I assigned 0 to mr-parms elements so it runs
without errors
But whe I tried the following line I copy and pasted from your
message:
mean=sum(Ps.*NU)/sum(Ps); ### I got the following error
Undefined function 'times' for input arguments of type 'struct'.
Any help?
Cheers, Marcos
PS: I promised I will post the final solution to list. But I guess it
is more didactic if these little problems are solved before.
TY, again.
Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu:
Hi Marcos,
the right way of doing this is using the soft posteriors to compute the
mean and variance, rather than thresholding at p=0.5. For instance, if
you wanted to compute the mean and variance of the intensitites of the
subiculum, you would do something like this:
mean=sum(Ps.*NU)/sum(Ps);
variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
(where Ps is the posterior of the subiculum)
Cheers,
/Eugenio
On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
Hi, Freesurfer Experts
After usual processing with recon-all -all we get the aseg.stats file
with several data including intensity values like:
normMean normStdDev
normMin normMax normRange
Left-Hippocampus 77.8939 7.574846.
105.59.
How could I get similar results for each hippocampal subfield,
assuming I also generated all posterior*.mgz files corresponding to
each subfield?
I guess I should first
Re: [Freesurfer] Hippocampal subfields intensity
Hi Marcos, the right way of doing this is using the soft posteriors to compute the mean and variance, rather than thresholding at p=0.5. For instance, if you wanted to compute the mean and variance of the intensitites of the subiculum, you would do something like this: mean=sum(Ps.*NU)/sum(Ps); variance=sum(Ps.*(NU-mean).^2)/sum(Ps); (where Ps is the posterior of the subiculum) Cheers, /Eugenio On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote: Hi, Freesurfer Experts After usual processing with recon-all -all we get the aseg.stats file with several data including intensity values like: normMean normStdDev normMin normMax normRange Left-Hippocampus 77.8939 7.574846. 105.59. How could I get similar results for each hippocampal subfield, assuming I also generated all posterior*.mgz files corresponding to each subfield? I guess I should first binarize each of the subfields file with a threshold=127 to map all the pertinent voxels, and then use these files as masks over nu.mgz and calculate the intensities values. But I do not know the best way to accomplish this after the binarize step. Thank you in advance for any help. Marcos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Hippocampal subfields intensity
Hi Marcos,
1. your fix of MRIread.m is great. I forgot of this bug; we should
totally take care of it.
2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
difference voxel space. So, you need to resample norm.mgz to the space
of the subfields. To do so, you can use mri_convert with the option -rl
(reslice like):
mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz
3. Now you can do:
A=MRIread('norm.mgz');
data=A.vol(:);
B=MRIread('posterior_subiculum.mgz');
post=double(B.vol(:));
mean=sum(data.*post)/sum(post);
variance=sum((data-mean).^2.*post)/sum(post);
Cheers,
/Eugenio
On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
Hi, Eugenio
TY for your fast help. I understood you were suggesting to compute
that on MatLab and I tried this:
NU=MRIread('nu.mgz')### that runs ok
Ps=MRIread('posterior_left_subiculum.mgz') ### it fails with the
following message
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bounds because
numel(mr_parms)=0.
Error in MRIread (line 100)
tr = mr_parms(1);
I solved creating a little customized nMRIread.m with the following
changes:
if numel(mr_parms) 0
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
else
mr_parms(1) = 0;
mr_parms(2) = 0;
mr_parms(3) = 0;
mr_parms(4) = 0;
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
end
With those changes I assigned 0 to mr-parms elements so it runs
without errors
But whe I tried the following line I copy and pasted from your
message:
mean=sum(Ps.*NU)/sum(Ps); ### I got the following error
Undefined function 'times' for input arguments of type 'struct'.
Any help?
Cheers, Marcos
PS: I promised I will post the final solution to list. But I guess it
is more didactic if these little problems are solved before.
TY, again.
Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu:
Hi Marcos,
the right way of doing this is using the soft posteriors to compute the
mean and variance, rather than thresholding at p=0.5. For instance, if
you wanted to compute the mean and variance of the intensitites of the
subiculum, you would do something like this:
mean=sum(Ps.*NU)/sum(Ps);
variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
(where Ps is the posterior of the subiculum)
Cheers,
/Eugenio
On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
Hi, Freesurfer Experts
After usual processing with recon-all -all we get the aseg.stats file
with several data including intensity values like:
normMean normStdDev
normMin normMax normRange
Left-Hippocampus 77.8939 7.574846.
105.59.
How could I get similar results for each hippocampal subfield,
assuming I also generated all posterior*.mgz files corresponding to
each subfield?
I guess I should first binarize each of the subfields file with a
threshold=127 to map all the pertinent voxels, and then use these
files as masks over nu.mgz and calculate the intensities values. But I
do not know the best way to accomplish this after the binarize step.
Thank you in advance for any help.
Marcos
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.
___
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.
Re: [Freesurfer] subfield algorithm and subject intensity differences
Dear Josh, at this point, and given that the boundaries between these subfields cannot really be seen in 1mm T1 scans, the algorithm assumes that all the subfields other than fimbria and fissure share the same image intensity properties. Therefore, using your own words: depend only on outward boundaries of the hippocampus and probability priors to determine the inner boundaries between CAs and dentate gyrus Cheers, /Eugenio - Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] hippocampal subfield segmentation
Title Automated segmentation of hippocampal subfields from ultra‐high resolution in vivo MRI Authors Koen Van Leemput, Akram Bakkour, Thomas Benner, Graham Wiggins, Lawrence L Wald, Jean Augustinack, Bradford C Dickerson, Polina Golland, Bruce Fischl Year 2009 Hippocampus Volume 19 Issue 6 Pages 549-557 On Wed, 2013-06-05 at 10:54 +0200, Claudia Dacquino wrote: Thank you for your response. Would you suggest a reference I can refer to? 2013/6/4 Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu I would probably leave out the fissure, but not the fimbria... Cheers, /Eugenio On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote: Hi guys! I have a dataset including hippocampal subfields obtained through the -hippo-subfields flag. I want to have a measure of total hippo volume and I'm not sure which structures should I include in the sum. I was thinking to exclude fimbria and fissure and sum the others. Am I right? Or should I simply sum all the structures? Any help is more than welcome Cheers, Fabrizio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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. -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] hippocampal subfield segmentation
I would probably leave out the fissure, but not the fimbria... Cheers, /Eugenio On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote: Hi guys! I have a dataset including hippocampal subfields obtained through the -hippo-subfields flag. I want to have a measure of total hippo volume and I'm not sure which structures should I include in the sum. I was thinking to exclude fimbria and fissure and sum the others. Am I right? Or should I simply sum all the structures? Any help is more than welcome Cheers, Fabrizio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Freeview automation
Ender asked me to forward you this: I had to automate freeview recently. Freeview can be used via command line. For options please write freeview -h in the console / terminal. An example command that produces a surface and overlays a map on it: freeview -f lh.inflated:overlay=L.mgz -cam azimuth 180 Let me know if this helps. Cheers, E On Fri, 2013-05-31 at 08:35 -0400, Ruopeng Wang wrote: There is a screenshot option -ss from the command-line. Run 'freeview -h' will show you all the available options. Ruopeng On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga gariko...@gmail.com wrote: Hi list, is it possible to automate Freeview automation from the command line? I want to automatically render 3D images of the hippocampus (I have a separate volume, based on hippo-subfields) and have an image for all subjects for quality checking. thanks! Gari ___ 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 -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] hipposubfields and data
Hi Josh, as of now, it uses nu.mgz, which is conformed and bias field corrected with N3. Koen, do you think we should add a flag to change this? The algorithm is pretty resolution-independent, and could certainly benefit from higher-res data. Cheers, /Eugenio On Tue, 2013-05-28 at 13:34 -0700, Joshua Lee wrote: I have read that the hippo-subfield algorithm uses the aseg for initialization, and then uses the original MRI data. By original, does that mean it up-samples the conformed 1mm data to .5mm, or does that mean it takes the original original input (i.e. my 0.7 mm isotropic MPRAGE) and upsamples it to .5mm? Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] QDEC and Hippocampal subfields
Hi Marcos, the hippocampal subfield volumes are single values for each subject and hemisphere, so you cannot display them on the brain surface. Cheers, /Eugenio On Thu, May 16, 2013 6:22 pm, Marcos Martins da Silva wrote: Hi, Doug Thank you for your answer. Well I guess that after I read your both tutorials for group analysis (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis ) I mistook the concepts of qdec.table.dat and FSGD. My fault. Following the QDEC tutorial I saw we could import aseg data to qdec.table.dat after pressing generate stats data tables button. So I was wondering if I could do the same from hippo-subfields data. Importing is faster and more precise than make the table by hand. Well the hippo-subfield pipeline creates several files such as posterior_left_subiculum.mgz on for each subfield and side. As far as I know you can: 1- run kvlQuantifyPosteriorProbabilityImages to output the volume in voxels 2- visualize the subfield segmentations with freeview loading nu.mgz and the posterior* files as p-labels. Following QDEC tutorial we could generate a display showing the correlation between cortical thickness (or volume) and age for example. I would like to a similar analysis with hippo-subfields and get a display showing the correlations of the hippo-subfields and age. So, just for an example, perhaps I could notice that subiculum volume decreases with age but hippocampal fissure increases with age. I guess I could analyze the data from hippo-subfields in a statistical package to get numbers and graphics but it would be great if I could see that as a surface like we do with cortical data. Cheers, Marcos Em Qui, 2013-05-16 Ã s 11:56 -0400, Douglas N Greve escreveu: Hi Marcos, On 05/15/2013 08:32 PM, Marcos Martins da Silva wrote: Hi, freesurfers I have two questions: 1- Is there a way to use QDEC to analyze data from hippocampal subfields created by recon-all -s subj -hippo-subfields? That is, I know I can manually put data from posterior* files when making the FSGD file but it would be great if I could import it like I do from aseg.stats. when you say you want analyze the hippo subfields in QDEC, do you mean you want to include them as regressors?If so, you will need to add them to your QDEC table. BTW, QDEC does not needan FSGD file. 2- Assuming all data from my subjects are already are already in the FSGD, I understand I can select cortical thickness or volume as dependent variable and inspect the correlations between cortical thickness and age, for example. But I could not find how to define a hippocampal subfield volume as a dependent variable. Is that possible? This way I could display correlations between a subfield volume and age or gender. I have not used the hippo subfields yet, and I'm embarrassed to say that I don't know what exactly it outputs. If there is a stats file there, you can run asegstats2table to create a table file, then use the table as input to mri_glmfit (use the --table option). doug Thank you, Marcos ___ 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 - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Hippo-subfields
Hi Marcos, the subfields of the left and right hippocampi are defined on different voxel spaces. If you want to combine them, you first need to reslice them to a common voxel space (for instance using -rl in mri_convert) Cheers, /Eugenio On Fri, April 19, 2013 9:57 pm, Marcos Martins da Silva wrote: TYVM, Juan Eugenio and Bruce. I am a neurologist and Professor in Federal University of Rio de Janeiro. I am confortable with Linux and scripts but, as a physician, eigenvectors will be really hard. I will try to get some help inside University. But if I correctly understood, it seems an elegant way to make tool that will work with several hippocampi with greater consistency than manual approach. Your step by step directions worked great, Juan. But I had to make a Left and a Right file. When I tried to concat right and left subfields in teh same file I got an error saying that right and left Ca1 dimensions did not match. Thank you again. Em Qui, 2013-04-18 Ã s 11:29 -0400, Juan Eugenio Iglesias escreveu: I agree with Bruce. You can use MRIread.m to read in the data. Regarding the other question: first you need to combine the posteriors of all the subfields into a single posterior for the whole hippocampus. You can do that like this: mri_concat posterior_fimbria.mgz posterior_CA1.mgz ... --sum --o posteriorWholeHippocampus.mgz Then you can threshold the posterior at probability 0.5 to obtain a binary hippocampal mask: mri_binarize --i posteriorWholeHippocampus.mgz --min 127 --o binaryHippocampalMask.mgz Finally, you can generate a surface by tesselating the mask: mri_tesselate binaryHippocampalMask.mgz 1 surfaceFile You can visualize the output with freeview -v posteriorWholeHippocampus.mgz -f surfaceFile Cheers, /Eugenio On Thu, 2013-04-18 at 11:22 -0400, Bruce Fischl wrote: Hi Marcos I would do it in matlab. Compute the spatial eigenvectors then divide the hippocampus up along the primary eigenvector cheers Bruce On Thu, 18 Apr 2013, Marcos Martins da Silva wrote: Thank you for your answer, Juan. Yes, I want a surface of the whole hippocampus and I thought I had just obtained that using freeview and adding all hippo-subfield files. That resulted in the screenshot I previously attached. I just do not know how I can save the resultant surface. After I checked show as isosurface in 3D view the low and high threshold controls appeared. The default threshold values on Freeview for low was 127.5 and high was 255. When I played with these controls, the size of the surfaces changed on 3D view. That is why I made the second question. I was trying to select the correct values for low and high threshoulds so I get an image consistent with the volume values we get after running kvlQuantifyPosteriorProbabilityImages. After setting the correct values I would like to save the work as a surface so I could load the whole surface instead of loading each individual subfield file. But I did not find a save as surface option. So I used the screenshot tool to save the work. This way I could at least show you what I got but I thought it was not the best way to do it. Relating to the last question about generating a new segmentation (anterior, body and posterior), you said I could use simple geometric rules to get it. Could you tell me where I can find instructions about how to do it? Sorry, I am afraid I am a novice here and my questions are the best proof of this, so I would like to thank you for all your patience. Em Qua, 2013-04-17 Ã s 21:19 -0400, Juan Eugenio Iglesias escreveu: Dear Marcos, 1- How do I save the combined 3D view I got as a surface? Do you want a surface of the whole hippocampus? In that case I would suggest adding up the probability volumes from all the subfields and thresholding the resulting volume. 2-I know the hippo-subifields .mgz files are probability maps and if I guess right kvlQuantifyPosteriorProbabilityImages read these files to count how many voxels you have in each subfield. I also guess it count only the voxels with reasonable high probability to be part of each subfield. If so, what is the minimum value between 1 and 255 the program use to decide if a particular voxel is valid? The estimates of the volumes are based on soft probabilities, so all voxels with non-zero probability contribute towards the estimate. For instance, a voxel with value 255 contributes to the volume 255 times as much as a voxel with a value of 1. 3- Is it possible to merge hippo-subfield .mgz files data and to generate a different segmentation like anterior (anterior quarter), body (the2 intermediate quarters) and posterior (posterior quarter). There are currently no scripts in FreeSurfer to generate such a partition. But you could always
Re: [Freesurfer] Hippo-subfields
I agree with Bruce. You can use MRIread.m to read in the data. Regarding the other question: first you need to combine the posteriors of all the subfields into a single posterior for the whole hippocampus. You can do that like this: mri_concat posterior_fimbria.mgz posterior_CA1.mgz ... --sum --o posteriorWholeHippocampus.mgz Then you can threshold the posterior at probability 0.5 to obtain a binary hippocampal mask: mri_binarize --i posteriorWholeHippocampus.mgz --min 127 --o binaryHippocampalMask.mgz Finally, you can generate a surface by tesselating the mask: mri_tesselate binaryHippocampalMask.mgz 1 surfaceFile You can visualize the output with freeview -v posteriorWholeHippocampus.mgz -f surfaceFile Cheers, /Eugenio On Thu, 2013-04-18 at 11:22 -0400, Bruce Fischl wrote: Hi Marcos I would do it in matlab. Compute the spatial eigenvectors then divide the hippocampus up along the primary eigenvector cheers Bruce On Thu, 18 Apr 2013, Marcos Martins da Silva wrote: Thank you for your answer, Juan. Yes, I want a surface of the whole hippocampus and I thought I had just obtained that using freeview and adding all hippo-subfield files. That resulted in the screenshot I previously attached. I just do not know how I can save the resultant surface. After I checked show as isosurface in 3D view the low and high threshold controls appeared. The default threshold values on Freeview for low was 127.5 and high was 255. When I played with these controls, the size of the surfaces changed on 3D view. That is why I made the second question. I was trying to select the correct values for low and high threshoulds so I get an image consistent with the volume values we get after running kvlQuantifyPosteriorProbabilityImages. After setting the correct values I would like to save the work as a surface so I could load the whole surface instead of loading each individual subfield file. But I did not find a save as surface option. So I used the screenshot tool to save the work. This way I could at least show you what I got but I thought it was not the best way to do it. Relating to the last question about generating a new segmentation (anterior, body and posterior), you said I could use simple geometric rules to get it. Could you tell me where I can find instructions about how to do it? Sorry, I am afraid I am a novice here and my questions are the best proof of this, so I would like to thank you for all your patience. Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu: Dear Marcos, 1- How do I save the combined 3D view I got as a surface? Do you want a surface of the whole hippocampus? In that case I would suggest adding up the probability volumes from all the subfields and thresholding the resulting volume. 2-I know the hippo-subifields .mgz files are probability maps and if I guess right kvlQuantifyPosteriorProbabilityImages read these files to count how many voxels you have in each subfield. I also guess it count only the voxels with reasonable high probability to be part of each subfield. If so, what is the minimum value between 1 and 255 the program use to decide if a particular voxel is valid? The estimates of the volumes are based on soft probabilities, so all voxels with non-zero probability contribute towards the estimate. For instance, a voxel with value 255 contributes to the volume 255 times as much as a voxel with a value of 1. 3- Is it possible to merge hippo-subfield .mgz files data and to generate a different segmentation like anterior (anterior quarter), body (the2 intermediate quarters) and posterior (posterior quarter). There are currently no scripts in FreeSurfer to generate such a partition. But you could always take a mask of the whole hippocampus (either from aseg.mgz of from the combination of all the subfields, like I mentioned in 1) and define some simple geometric rules to create it. Kind regards, Eugenio TY in advance ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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
Re: [Freesurfer] Hippo-subfields
Dear Marcos, 1- How do I save the combined 3D view I got as a surface? Do you want a surface of the whole hippocampus? In that case I would suggest adding up the probability volumes from all the subfields and thresholding the resulting volume. 2-I know the hippo-subifields .mgz files are probability maps and if I guess right kvlQuantifyPosteriorProbabilityImages read these files to count how many voxels you have in each subfield. I also guess it count only the voxels with reasonable high probability to be part of each subfield. If so, what is the minimum value between 1 and 255 the program use to decide if a particular voxel is valid? The estimates of the volumes are based on soft probabilities, so all voxels with non-zero probability contribute towards the estimate. For instance, a voxel with value 255 contributes to the volume 255 times as much as a voxel with a value of 1. 3- Is it possible to merge hippo-subfield .mgz files data and to generate a different segmentation like anterior (anterior quarter), body (the2 intermediate quarters) and posterior (posterior quarter). There are currently no scripts in FreeSurfer to generate such a partition. But you could always take a mask of the whole hippocampus (either from aseg.mgz of from the combination of all the subfields, like I mentioned in 1) and define some simple geometric rules to create it. Kind regards, Eugenio TY in advance ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] R: Re: R: Re: hippo subfield
. If these steps do not solve the issue for you, please respond with a the exact error you receive. Hope this helps. -Zeke On 03/22/2013 12:00 PM, std...@virgilio.it wrote: I'm running: recon-all -s Diff02 -hippo-subfields with the following error. Thanks. Stefano Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff02 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 Stefano wheel 49 Mar 22 16:53 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 # #@# Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013 \n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \n Doing left side meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz subjectName: Diff02 side: left inputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02 outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults directory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already exists directory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already exists cd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm . cp /Applications/freesurfer/data/GEMS/imageDump.mgz . kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 *failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.02550.00940.9996 -3.1939* *Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64* * * *recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013* For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer
Re: [Freesurfer] R: Re: R: Re: R: Re: hippo subfield
://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 - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] R: Re: hippo subfield
Hi Stefano, From the command line, type: ldd kvlApplyTransform and send us the output that you get. Cheers, /Eugenio On Fri, 2013-03-22 at 18:44 +0100, std...@virgilio.it wrote: I'm sorry but, what's meaning ldd kvlApplyTransform? What's I should do more simply? Stefano Messaggio originale Da: k...@nmr.mgh.harvard.edu Data: 22-mar-2013 18.22 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield Hi Stefano, Can you do ldd kvlApplyTransform and send us the result? Koen On 3/22/13, std...@virgilio.it std...@virgilio.it Hippocampal Subfields processing Fri Mar 22 16:56:31 CET 2013\n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults\n kvlSegmentHippocampalSubfields.sh Diff02 left /Applications/freesurfer/subjects/subject_prova/Diff02 /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults \nDoing left sidemeshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gzcompressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txtboundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgzsubjectName: Diff02side: leftinputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResultsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02 already existsdirectory /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/left already existscd /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/tmp/subfieldResults/Diff02/leftcp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/nu.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/aseg.mgz .cp -f /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/mri/transforms/talairach.xfm .cp /Applications/freesurfer/data/GEMS/imageDump.mgz .kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found/Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 77530 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.0255 0.00940.9996 -3.1939Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff02 exited with ERRORS at Fri Mar 22 16:56:31 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff02/Diff02/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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 -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question about hippocampus subfield segmentation flag
Hi Mehul, that should work. Let us know if you have any problems. Kind regards, Juan Eugenio Iglesias On Sat, 2013-03-16 at 14:29 -0700, Mehul Sampat wrote: Hi Folks, I had a question about the hippocampus subfield segmentations as described here : http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I am planning to use this processing outline: 1. recon-all -s subject -autorecon1 -autorecon2 2. add control points 3. recon -all -s subject -autorecon2-cp 4. recon -all -s subject -autorecon3 -hippo-subfields Is this permissible or do I need to need to introduce the -hippo-subfields flag earlier. Thanks Mehul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Hippocampus volume calculations
Dear Gari, The subfield module uses a different, independent method to segment the hippocampus, and consistency with ASEG results is not explicitly enforced. That said, the subfield module is inialialized with the ASEG, and the results should be pretty close to each other, for the most part. Have you visually inspected the segmentation for those cases in which the difference looks large? Thanks, /Eugenio On Mon, 2013-02-25 at 14:10 +0100, Garikoitz Lerma-Usabiaga wrote: Hi, I am calculating hippocampus volumes with 5.2 in CentOS 4. I compare volumes (the same apply for lh and for rh) when calculating as: Left.Hippocampus value in 1mm3 from aseg.stats I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in order to get mm3, and sum every column except left_hippocampal_fissure. I obtain quite different values, for example: row.names lh.aseg lhHIP rh.aseg rhHIP 1 S_00 4848.8 3828.187 4878.8 3767.739 2 S_02 4153.8 3371.517 4547.6 3389.918 Am I doing anything wrong? Should I calculate the hippos subfields volumes differently? Many thanks! Gari ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] nb0 question
Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter where in the table it is. From the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Step7.3: Specifying Number Of low-b Images The last step to set up if not using original DICOMs would be to specify the number of low-b images with the following variable: set nb0 = *No. of low-b images* ** - To be replaced with the actual number from the acquisition. On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote: Hi list, I'm running TRACULA. I do not have problem when I have 16 DTI direction and b=0 is the first volume: I put nb0=1. For some subjects I have 16 direction but b=0 is the last of volume in dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to position of b=0 in the bvals.txt or to total number (quantitative) of b=0 in the bvals.txt? Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] nb0 question
Of course! But, if I understood correctly, Stefano only has one, either at the beginning of the end of the gradient table, and in both cases nb0=1 Cheers, /Eugenio On Thu, February 21, 2013 12:20 pm, Shantanu Ghosh wrote: Hi Juan, The number of b0 images can be more than 1; it is specified when you acquire the image. Hth, Shantanu On Thu, February 21, 2013 12:16 pm, Juan Eugenio Iglesias wrote: Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter where in the table it is. From the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Step7.3: Specifying Number Of low-b Images The last step to set up if not using original DICOMs would be to specify the number of low-b images with the following variable: set nb0 = *No. of low-b images* ** - To be replaced with the actual number from the acquisition. On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote: Hi list, I'm running TRACULA. I do not have problem when I have 16 DTI direction and b=0 is the first volume: I put nb0=1. For some subjects I have 16 direction but b=0 is the last of volume in dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to position of b=0 in the bvals.txt or to total number (quantitative) of b=0 in the bvals.txt? Thanks, Stefano ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School Massachusetts General Hospital Martinos Center for Biomedical Imaging - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Hippocampus volume
Hi again, like I said in my previous emails, the measurements from the subfield tools are based on .5x.5x.5 voxels, so you have to divide them by 8 to convert them to cubic milliliters. Then, if you add up the volumes from the subfields (without including the hippocampal fissure), you should get something close to the measurement based on aseg.mgz (2166). Kind regards, Eugenio On Thu, December 6, 2012 10:41 am, Antonella Kis wrote: Dear FS team, After I ran the recon-all to get the total cortical thickness, the volume of the left hypocampus ( = the number of voxels) equals to 2166 which I thought should be the total hippocampal volume. But if we add all the voxel numbers from the hippocampal subfield I will get a much larger number so I wonder which one represents the true total volume in terms of number of voxels. Can you also please advise how can I get differentiated hipocampus segmentation in form of head and body. Thank you. Antonella___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] Head, body and tail of hippocampus
Hi Antonella, The volume given by the hippocampal subfield tool is in .5x.5x.5 voxels. Therefore, to convert to cubic millimeters, you need to divide by 8. Regarding the sufield - A/P question, the only correpondance is Left-Hippocampus - left tail and Right-Hippocampus-right tail Cheers, /Eugenio On Tue, 2012-12-04 at 08:22 -0800, Antonella Kis wrote: Dear FS team, I would like to know which subfield ( left_presubiculum, left_CA1, left_CA2-3, left_fimbria, left_subiculum, left_CA4-DG, left_hippocampal_fissure) contribute to the head, body and tail of left hippocampus. It also seems that the first column of nonPartialVolumeStatsLeft.txt file contains the total volume of the left hippoccampus but based on the numbers (I copied them below) the total volume is smaller than the volume of some of teh subfileds. How this is possible? volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissure C231681.22564.291405.073814.14211.792 2983.062118.63422.786 Thank you. Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
Re: [Freesurfer] hippocampal subfield segmentation
Hi Antonella, Just run recon-all with the flag -hippo-subfields but without the flag -all (otherwise you'll be rerunning a lot of stuff you do not need to rerun): DO: recon-all -s bert -hippo-subfields DON'T DO: recon-all -s bert -all -hippo-subfields Kind regards, /Eugenio On Mon, 2012-12-03 at 08:39 -0800, Antonella Kis wrote: Dear FS team, I would like to know if there is any options to get the hippocampal subfield segmentation so I can get the volume for each segmentation if I was running only recon-all for all my subjects or I need to re-run recon-all but with a hippocampal subfield segmentation option this time? Many thanks, Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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.
