[Freesurfer] Hippocampal volume estimation
Hello, I have to segment out hippocampus only and calculate its volume. Since FreeSurfer segments out many sub-cortical structures and their respective volumes, it takes a lot of time ( more than 10 hours ). Is there any way to extract a particular sub-cortical structure only from brain ( hippocampus in my case ) without taking a lot of time? Thank you ___ 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] TRACULA error: pre-processing
Hi, I have a problem running TRACULA in the pre-processing stage. The error message is the following; Loading streamline start ROI from /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz niiRead(): error opening file /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz ERROR: Could not read /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Linux localhost.localdomain 2.6.18-371.1.2.el5 #1 SMP Tue Oct 22 12:51:53 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at 2014. 01. 23. (목) 18:32:17 KST I guess this error started to happen after I updated Freesurfer version 5.3.0 (I could successfully run TRACULA with same data with the prior version of Freesurfer) In my setting, $TUTORIAL_DATA -- /usr/local/freesurfer/subjects/tracula/tutorialdata I tried re-download the file, diffusion_tutorial.tar.gz, from freesurfer server and extracted file again, but still I couldn't find the file lh.cst_AS_roi1.flt.nii.gz in Diff001/dlabel/mni folder. Thank you in advance for your advice. Wonsang Jung ___ 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 volume estimation
no, sorry. The contextual information from segmenting everything helps a lot in improving accuracy, so there is no way to only segment a single structure. cheers Bruce On Thu, 23 Jan 2014, Tanya Verma wrote: Hello, I have to segment out hippocampus only and calculate its volume. Since FreeSurfer segments out many sub-cortical structures and their respective volumes, it takes a lot of time ( more than 10 hours ). Is there any way to extract a particular sub-cortical structure only from brain ( hippocampus in my case ) without taking a lot of time? Thank you ___ 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] Time taken by Freesurfer for processing
Hi, I would like to ask that why does the Freesurfer takes so much time for processing particularly autorecon2 ? Knowing that Freesurfer takes a lot of time for processing, why is it still used widely by researchers ? For segmentation followed by volume calculation , does one has to really wait for hours for the results? Thank you ___ 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] Time taken by Freesurfer for processing
Hi Tanya we have always preferenced minimizing manual interactions over computer time. It takes so long because of its level of automation and its completeness. This is also why it is so widely used I assume - because it generates a comprehensive, accurate and automated morphometric assay of the human brain. Seems like waiting a few extra hours to get something complete, automated and accurate isn't a big deal. cheers Bruce On Thu, 23 Jan 2014, Tanya Verma wrote: Hi, I would like to ask that why does the Freesurfer takes so much time for processing particularly autorecon2 ? Knowing that Freesurfer takes a lot of time for processing, why is it still used widely by researchers ? For segmentation followed by volume calculation , does one has to really wait for hours for the results? Thank you ___ 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] Time taken by Freesurfer for processing
Newer versions also have the ability to run some stages on multiple CPU cores (with the -openmp cores flag) which speeds certain stages (e.g. in autorecon2) up considerably. I'm also sure Bruce wouldn't turn down more resources to hire the programmers needed to make it faster either! Peace, Matt. On 1/23/14 11:25 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanya we have always preferenced minimizing manual interactions over computer time. It takes so long because of its level of automation and its completeness. This is also why it is so widely used I assume - because it generates a comprehensive, accurate and automated morphometric assay of the human brain. Seems like waiting a few extra hours to get something complete, automated and accurate isn't a big deal. cheers Bruce On Thu, 23 Jan 2014, Tanya Verma wrote: Hi, I would like to ask that why does the Freesurfer takes so much time for processing particularly autorecon2 ? Knowing that Freesurfer takes a lot of time for processing, why is it still used widely by researchers ? For segmentation followed by volume calculation , does one has to really wait for hours for the results? Thank you ___ 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] mri_surfcluster
Hi all, I have obtained laterality indices using xhemi analyses and would like to use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions. I know to get the FDR threshold from tksurfer, but I want to restrict the clusters to a certain cluster size. Based on a previous thread ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html ) I think this should be done using mri_surfcluster but I am having trouble with the actual commands. I've tried this but it doesn't seem to work: mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf fsaverage_sym --hemi lh the error = srcsubjid must be supplied If I'm performing this on a group file (not individual subject), what would I even input as the subjid? Or do I have this totally wrong? Thanks! Krista ___ 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] mri_surfcluster
just add --subject fsaverage_sym btw, that command does not perform FDR doug On 01/23/2014 01:41 PM, krista kelly wrote: Hi all, I have obtained laterality indices using xhemi analyses and would like to use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions. I know to get the FDR threshold from tksurfer, but I want to restrict the clusters to a certain cluster size. Based on a previous thread ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html ) I think this should be done using mri_surfcluster but I am having trouble with the actual commands. I've tried this but it doesn't seem to work: mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf fsaverage_sym --hemi lh the error = srcsubjid must be supplied If I'm performing this on a group file (not individual subject), what would I even input as the subjid? Or do I have this totally wrong? Thanks! Krista ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] poor grey/white distinction in superior part of scan
Hello, I am emailing to inquire about whether poor grey/white contrast in one part of a scan (i.e., the posterior and superior part of the scan; ~parietal cortex) can be addressed. The contrast in other parts of the scan looks good and freesurfer does a great job of distinguishing white from grey. For the parietal cortex area the cortex appears very thin. In addition, the entire brain appears 'white' or bright, even though the brain doesn't look this bright if you reconstruct it from dicoms. We have now obtained 4 scans like this, so it isn't just one person with thinning cortex. How can I make an adjustment to only this superior part of the brain and leave the rest of it alone? Or do I need to make an adjustment to the intensity early on for the entire scan and then basically start over with editing? Best, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego ___ 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] poor grey/white distinction in superior part of scan
Some pictures would probably be helpful to know what the issue is. Peace, Matt. From: Christine Smith cnsm...@ucsd.edu Date: Thursday, January 23, 2014 1:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] poor grey/white distinction in superior part of scan Hello, I am emailing to inquire about whether poor grey/white contrast in one part of a scan (i.e., the posterior and superior part of the scan; ~parietal cortex) can be addressed. The contrast in other parts of the scan looks good and freesurfer does a great job of distinguishing white from grey. For the parietal cortex area the cortex appears very thin. In addition, the entire brain appears 'white' or bright, even though the brain doesn't look this bright if you reconstruct it from dicoms. We have now obtained 4 scans like this, so it isn't just one person with thinning cortex. How can I make an adjustment to only this superior part of the brain and leave the rest of it alone? Or do I need to make an adjustment to the intensity early on for the entire scan and then basically start over with editing? Best, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Help Thickness Reproducibility
Dear FreeSurfers I am having some troubles to run step 4 of protocol to thickness reproducibility. The error message is below: nf04:~ mris_surface_stats -nsmooth 100 -surf_name /home/nf04/subjects/t_pac01/su rf/lh.white -out_name /home/nf04/subjects/groupstudy/lh_std_60.mgh -absmean /home/nf04/subjects/groupstudy/lh_absmean_60.mgh -mean /home/nf04/subjects/groupstudy/lh_mean_60.mgh -absstd /home/nf04/subjects/groupstudy/lh_absstd_60.mgh /home/nf04/subjects/groupstudy/tpac02_lh_thicknes_diff_resampled_to_tpac01.mgh Perform 100 steps of smoothing of input data using /home/nf04/subjects/groupstudy/lh_std_60.mgh as output file using /home/nf04/subjects/groupstudy/lh_absmean_60.mgh as output file for abs-mean using /home/nf04/subjects/groupstudy/lh_mean_60.mgh as output file for mean using /home/nf04/subjects/groupstudy/lh_absstd_60.mgh as output file for std-of-abs-mean reading /home/nf04/subjects/groupstudy/tpac02_lh_thicknes_diff_resampled_to_tpac01.mgh... Smooth input data by 100 steps ERROR: MyMRISsmooth: Surf/Src dimension mismatch Stats over surface (76117 vertices): mean = 0.368766, std = 1.02826, absmean = 0.790395, absstd = 0.754038 I would appreciate so much any help. Many thanks Thiago Junqueira Medical Physicist, Msc Student in Neuroimage Neuroimage Lab and Medical Physics Lab University of Campinas Phone: +55 19 8809-9476 ___ 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] mri_surfcluster
Thanks Doug! I realize this doesn't do FDR but I've gotten the FDR threshold from tksurfer and will use that as my -thmin. One last thing, how would I view the results of mri_surfclluster in tksurfer? Would I load the ocn.mgh file? If so, I can't seem to find it. On Thu, Jan 23, 2014 at 2:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: just add --subject fsaverage_sym btw, that command does not perform FDR doug On 01/23/2014 01:41 PM, krista kelly wrote: Hi all, I have obtained laterality indices using xhemi analyses and would like to use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions. I know to get the FDR threshold from tksurfer, but I want to restrict the clusters to a certain cluster size. Based on a previous thread ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html ) I think this should be done using mri_surfcluster but I am having trouble with the actual commands. I've tried this but it doesn't seem to work: mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf fsaverage_sym --hemi lh the error = srcsubjid must be supplied If I'm performing this on a group file (not individual subject), what would I even input as the subjid? Or do I have this totally wrong? Thanks! Krista ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_surfcluster
there are lots of output. You can create an annotation (--oannot), labels (--olab), copy the input and set nonclusters to 0 (--o), map of corrected voxel-wise significances (--vwsig), or map of cluster-wise significances (--cwsig). Of course you can get a simple table of the output too (--sum) doug On 01/23/2014 02:43 PM, krista kelly wrote: Thanks Doug! I realize this doesn't do FDR but I've gotten the FDR threshold from tksurfer and will use that as my -thmin. One last thing, how would I view the results of mri_surfclluster in tksurfer? Would I load the ocn.mgh file? If so, I can't seem to find it. On Thu, Jan 23, 2014 at 2:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: just add --subject fsaverage_sym btw, that command does not perform FDR doug On 01/23/2014 01:41 PM, krista kelly wrote: Hi all, I have obtained laterality indices using xhemi analyses and would like to use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions. I know to get the FDR threshold from tksurfer, but I want to restrict the clusters to a certain cluster size. Based on a previous thread ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html ) I think this should be done using mri_surfcluster but I am having trouble with the actual commands. I've tried this but it doesn't seem to work: mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf fsaverage_sym --hemi lh the error = srcsubjid must be supplied If I'm performing this on a group file (not individual subject), what would I even input as the subjid? Or do I have this totally wrong? Thanks! Krista ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Help Thickness Reproducibility
The dimension mismatch means that the input data does not match the surface. It looks like the surface is from an individual but the input data is from a group analysis (which means fsaverage subject) On 01/23/2014 02:35 PM, Thiago Junqueira wrote: Dear FreeSurfers I am having some troubles to run step 4 of protocol to thickness reproducibility. The error message is below: nf04:~ mris_surface_stats -nsmooth 100 -surf_name /home/nf04/subjects/t_pac01/su rf/lh.white -out_name /home/nf04/subjects/groupstudy/lh_std_60.mgh -absmean /home/nf04/subjects/groupstudy/lh_absmean_60.mgh -mean /home/nf04/subjects/groupstudy/lh_mean_60.mgh -absstd /home/nf04/subjects/groupstudy/lh_absstd_60.mgh /home/nf04/subjects/groupstudy/tpac02_lh_thicknes_diff_resampled_to_tpac01.mgh Perform 100 steps of smoothing of input data using /home/nf04/subjects/groupstudy/lh_std_60.mgh as output file using /home/nf04/subjects/groupstudy/lh_absmean_60.mgh as output file for abs-mean using /home/nf04/subjects/groupstudy/lh_mean_60.mgh as output file for mean using /home/nf04/subjects/groupstudy/lh_absstd_60.mgh as output file for std-of-abs-mean reading /home/nf04/subjects/groupstudy/tpac02_lh_thicknes_diff_resampled_to_tpac01.mgh... Smooth input data by 100 steps ERROR: MyMRISsmooth: Surf/Src dimension mismatch Stats over surface (76117 vertices): mean = 0.368766, std = 1.02826, absmean = 0.790395, absstd = 0.754038 I would appreciate so much any help. Many thanks Thiago Junqueira Medical Physicist, Msc Student in Neuroimage Neuroimage Lab and Medical Physics Lab University of Campinas Phone: +55 19 8809-9476 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] converting binary cortical GM ribbon mask to mative T1 space
Hi, We'd like to map the cortical GM ribbon on our original single volume native space anatomical T1. The dataset has been run through recon-all -all. The 'rawavg.mgz' or '001.mgz' is the native space T1 and 'ribbon.mgz' is the cortical GM mask in freesurfer space, correct? I converted the ribbon.mgz to native T1 space using: mri_label2vol --seg ribbon.mgz --temp rawavg.mgz --o ribbon-in-rawavg.mgz --regheader ribbon.mgz Is this the correct procedure? Thanks. Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ 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] Corrections to the segmentation lead to giant defects
Hi Thomas when you say errors in the hippocampus do you mean the aseg or the surfaces? If the surfaces, don't worry about them as they are not used in the hippocampal region. You are probably connecting the temporal lobe to the main body of the white matter creating a giant defect. cheers Bruce On Mon, 20 Jan 2014, Thomas Fink wrote: Dear Freesurfer experts, We are using FS 5.1 and have several participants with errors in the segmentation of the hippocampus and other regions of the cortex. So far we did corrections to the hippocampus but in 10 out of 13 participants we got error messages listed below: Seven participants: - CORRECTING DEFECT 0 (vertices=74686, convex hull=1605) Excessive topologic defect encountered: could not allocate 390335770 edges for retessellation Cannot allocate memory Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 - One participant: - mhtVoxelList_Add(189, 240, 290, 260205): complete list too big! mhtVoxelList_Add(189, 240, 290, 260205): complete list too big! No such file or directory marking ambiguous vertices... Too many intersected faces for face 255461 (126442, 128896, 128873) No such file or directory Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 - One participant: - CORRECTING DEFECT 14 (vertices=33317, convex hull=1285) mris_fix_topology(26738) malloc: *** mmap(size=1212047360) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 - One participant: - Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 414500 ambiguous faces found in tessellation segmenting defects... Bus error Darwin NPSY.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 - The error log says in all cases that there is something wrong with the cerebellum. When we open the ?h inflated.nofix file then we see the cerebellum added (see attached file) in the hemisphere we made the edits. We have no clue if or what we are doing wrong and here are the steps we did: - open the files (tkmedit subject norm.mgz -aseg.mgz - Tool - Configure Segmentation Brush info - select the hippocampus - add voxels - File - save segmentation - run recon with recon-all -autorecon2 -noaseg –autorecon3 -subjid subject -nuintensitycor-3T So far we had no problems with our subjects for all the previous steps (recon after wm, pial, edits) and it did run smoothly. Any help would be greatly appreciated. Thomas Fink Mail: thomas.f...@psy.lmu.de ___ 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] -qcache / fsaverage / number of vertices errors
Hi Mihaela usually that means the subject was partially but not completely rerun. You can try using recon-all -s subject -make all and see if it fixes it cheers Bruce On Thu, 23 Jan 2014, Mihaela Stefan wrote: Hello FreeSurfers, I am trying to run a group analysis with Qdec following thistutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnal ysis_freeview I got a series of errors when I ran: recon-all -s subjid -qcache ERROR: number of vertices in /home/subiculum/Desktop/local_recons/OCD_analysis/3662/surf/lh.volume does not match surface (126049,126592) ERROR: reading curvature file ... mri_concat ./tmp.mris_preproc.6022/3662.1.mgh --o lh.volume.fsaverage.mgh mghRead(./tmp.mris_preproc.6022/3662.1.mgh, -1): could not open file ninputs = 1 Checking inputs ERROR: reading ./tmp.mris_preproc.6022/3662.1.mgh ... Reading source surface reg/home/subiculum/Desktop/local_recons/OCD_analysis/fsaverage/surf/lh.sphere. reg Loading source data ERROR: could not read lh.volume.fsaverage.mgh as type 3 Linux subiculum-Precision-T1650 3.5.0-45-generic #68~precise1-Ubuntu SMP Wed Dec 4 16:18:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3662 exited with ERRORS at Thu Jan 23 15:22:21 EST 2014 One of the errors says number of vertices in... does not match surface. I found an older post where someone else was complaining about the same error and Doug suggested running recon-all -surfvolume ... https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-September/025737 .html I did that and then I ran -qcache again but I got the same errors. It also seems to be a problem with fsaverage. I do have a copy of fsaverage in the subject's directory of this study. I am attaching the log file with details about the errors. Can someone help me sort this out? Thank you, Mihaela ___ 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] Fwd: QDEC error
-- Forwarded message -- From: Wanda Truong wanda.truong...@gmail.com Date: 23 January 2014 16:57 Subject: QDEC error To: freesurfer@nmr.mgh.harvard.edu Hello, I am having trouble with my group analysis using QDEC. I have 3 groups, 72 subjects, and 4 covariates. This is the error I get: Loading data table /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/qdec.table.dat... Number of columns: 438 fsid column:1 Number of factors: 437 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. I've attached my qdec.table.dat file and fsgd file as well. I initially created the columns using excel and I copied and pasted it into a .txt. file. Could this be the problem? If so, what would be a better method? Thanks very much, Wanda -- Wanda Truong, MSc -- Wanda Truong, MSc qdec.table.dat Description: Binary data finalgroupanalysis.fsgd Description: Binary data ___ 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] Fwd: QDEC error
there is something wrong with the format. did you make your qdec table on a windows machine? If so, convert it to linux format or recreate it on a linux/mac machine doug On 01/23/2014 07:02 PM, Wanda Truong wrote: -- Forwarded message -- From: *Wanda Truong* wanda.truong...@gmail.com mailto:wanda.truong...@gmail.com Date: 23 January 2014 16:57 Subject: QDEC error To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Hello, I am having trouble with my group analysis using QDEC. I have 3 groups, 72 subjects, and 4 covariates. This is the error I get: Loading data table /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/qdec.table.dat... Number of columns: 438 fsid column:1 Number of factors: 437 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. I've attached my qdec.table.dat file and fsgd file as well. I initially created the columns using excel and I copied and pasted it into a .txt. file. Could this be the problem? If so, what would be a better method? Thanks very much, Wanda -- Wanda Truong, MSc -- Wanda Truong, MSc ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] FW: poor grey/white distinction in superior part of scan
From: Christine Smith cnsm...@ucsd.edu Date: Thursday, January 23, 2014 3:58 PM To: Matt Glasser m...@ma-tea.com Subject: Re: [Freesurfer] poor grey/white distinction in superior part of scan Please note that the left and right sides of the brain are flipped for freesurfer vs the dicom picture. Please find attached a dicom picture that is oriented the same way as freesurfer. Sorry for any confusion. On Thu, Jan 23, 2014 at 1:56 PM, Christine Smith cnsm...@ucsd.edu wrote: Dear Matt, Please find attached two pictures. One is of the brain from reconstructed dicom files (using AFNI). The other one is a pic from tkmedit of the same subject and approximately the same slice of brain. Notice that the freesurfer image is very bright. Look at the white matter and pial lines (i.e., cortical thickness) in the upper left hand part of the image and see how thin the cortex appears. Notice also, that there is very little grey/white contrast in this same area in the brain image reconstructed from dicoms. Please let me know if there are any other pictures you might desire or information you might need. Christine On Thu, Jan 23, 2014 at 11:33 AM, Matt Glasser m...@ma-tea.com wrote: Some pictures would probably be helpful to know what the issue is. Peace, Matt. From: Christine Smith cnsm...@ucsd.edu Date: Thursday, January 23, 2014 1:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] poor grey/white distinction in superior part of scan Hello, I am emailing to inquire about whether poor grey/white contrast in one part of a scan (i.e., the posterior and superior part of the scan; ~parietal cortex) can be addressed. The contrast in other parts of the scan looks good and freesurfer does a great job of distinguishing white from grey. For the parietal cortex area the cortex appears very thin. In addition, the entire brain appears 'white' or bright, even though the brain doesn't look this bright if you reconstruct it from dicoms. We have now obtained 4 scans like this, so it isn't just one person with thinning cortex. How can I make an adjustment to only this superior part of the brain and leave the rest of it alone? Or do I need to make an adjustment to the intensity early on for the entire scan and then basically start over with editing? Best, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listin fo/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. -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego attachment: dicom_flipped.jpg___ 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] (no subject)
Hi freesurfer crew, I found some details through this website http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/index.htm about cortical thickness maps with freesurfer. I have done some reading but can't really make much sense of how I might do this for a single subject through freesurfer. I have already done autorecon 2 and 3 and so have the cortical thickness stats but would like to put it into a map such as this one: [image: [Click to enlarge image]]http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/figs/FS.jpg Could you possibly advise on how I might go about this? Would be much appreciated. Many thanks and all the best, Hugh ___ 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] defect_labels to volume
Is there a way of making a volume like aparc+aseg with the defect labels so that cortical region where the defects are show up red? Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.auhttp://www.mcri.edu.au/ E chris.adam...@mcri.edu.au T 03 9936 6780 __ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com _ 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.
