Re: [Freesurfer] brain mask and T1 are not the same size
I also tried on a different computer with a different operating system (Yosemite) the manual corrections for the skull stripping and the same problem persists (dimension of the modified T1 changes to 255 x 255 x 256). Any ideas regarding how I can do these modifications for those 4 participants? Thank you in advance for your help, Isabelle * Isabelle Deschamps, Chercheure postdoctorale, Faculté de Médecine Département de réadaptation Université Laval Pavillon Ferdinand-Vandry 1050 avenue de la Médecine Québec (Québec) G1V 0A6 Centre de Recherche de l'Institut universitaire en santé mentale de Québec (CRIUMSQ) 2601, chemin de la Canardière, bureau F-2424A Québec (Québec) G1J 2G3 Téléphone : 418 663-5000 poste 6857 On Aug 5, 2016, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: TRACULA tract endpoints on cortical surface (Barbara Kreilkamp) 4. recent problems with hippocampal subfield and brainstem modules (Iglesias, Eugenio) 5. Registration of low-resolution EPI time series to CVS MNI (avoiding resampling) (Heidi Grohn) 6. Spearman correlation in FreeSurfer (martina.papme...@puk.unibe.ch) 7. Error using LGI script despite making suggested changes to Matlab script. (Sam Mathias) 8. Re: Spearman correlation in FreeSurfer (Douglas N Greve) 9. Re: How does Optseq ___ 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] resample structural ROI in functional space?
Hi All, I have a set of ROIs that were created in structural space, currently saved as volume masks. I would like to transform these into functional space, re-sampled to the functional resolution. Can anyone suggest a good way to do this? -kami Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office. ___ 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: TRACULA re-init error
Dan From: Ostrowski, Lauren Sent: Monday, August 08, 2016 4:08 PM To: Song, Daniel Subject: FW: TRACULA re-init error From: Ostrowski, Lauren Sent: Monday, August 08, 2016 4:04 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: TRACULA re-init error Hi all, I'm running into a problem with TRACULA, when I try to re-initialize tracts that failed to reconstruct during the first run. I have set reinit = 1 in the configuration file and specified the particular tracts that I want to reconstruct, but when I try to run the "trac-all -prior" step, I keep getting this error message: INFO: SUBJECTS_DIR is /autofs/cluster/neuromind/cat/bects/subjects INFO: Diffusion root is /cluster/neuromind/cat/bects/subjects/pBECTS001/trac Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/dev trac-preproc -c /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/dmrirc.local -log /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/trac-all.log -cmd /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/trac-all.cmd #- /usr/local/freesurfer/dev/bin/trac-preproc #- #@# Priors Mon Aug 8 15:53:46 EDT 2016 /usr/local/freesurfer/dev/bin/dmri_train --outdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni --out fmajor_PP_avg33_mni_bbr --slist /tmp/subj33.pBECTS001.15581.txt --trk dlabel/mni/fmajor_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 --rois dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz --bmask /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz --cptdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff --reg /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc ERROR: fio_pushd: /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni cwd /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/dlabel/mni cmdline /usr/local/freesurfer/dev/bin/dmri_train --outdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni --out fmajor_PP_avg33_mni_bbr --slist /tmp/subj33.pBECTS001.15581.txt --trk dlabel/mni/fmajor_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 --rois dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz --bmask /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz --cptdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff --reg /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc sysname Linux hostname truffles machine x86_64 user lo941 Output directory: /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni Output directory in test subject's space: /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff Output base: fmajor_PP_avg33_mni_bbr Training subject directory list: /tmp/subj33.pBECTS001.15581.txt Location of streamline files relative to base: dlabel/mni/fmajor_PP.bbr.trk Location of start ROI files relative to base: dlabel/mni/fmajor_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/fmajor_PP_roi2.bbr.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux truffles 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Aug 8 15:53:46 EDT 2016 Any help would be very much appreciated. It seems to me that TRACULA can't find the aparc+aseg labels, but when I looked at the aparc+aseg nifty file, the parcellations and labels all seem correct. Thanks, Lauren Ostrowski ___ 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] hippocampus question
Dear Freesurfer, I have noticed that the subcortical grey matter volume output for the hippocampus differs slightly from other segmentation methods, I was wondering if this is due to what subfields of the hippocampus are included in the segmentation. I was curious which subfields Freesurfer includes as regional boundaries for the hippocampus. Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ 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.
