[Freesurfer] FDR clustr-level Correction
Hi Freesurfer experts I am doing FS-nonlinear volume based FC analysis with cluster-level correction. 1. Could you please point me which command can do the FDR cluster-level Correction? 2. If i do correction using MonteCalo cluster-based correction. Is it right like the following command mri_glmfit-sim --glmdir g2v0 --sim mc-z 1 1.3 mc-z 1.3 --cwp 0.05 --sim-sign abs. It seems like the MonteCalo cluster-based correction cost long long time. thank you very much! Meiling___ 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
Page up / page down should work Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:16:13 PM Subject: [Freesurfer] Freeview Hi Freesurfers, I can’t change the current slice in freeview using the Up or Down key as described in the Freesurfer wiki. Instead the Up/Down key are moving the current slice up or down and not changing the current slice. Is there any shortcut that can change the current slice instead of the Up/ Down keys Thanks Mohamad ___ 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] F test results
Dear experts, I have 3 groups (A, PC, HC) and IQ as cov and I tried to do a F test on the cortical thickness but the output doesn't make sense as it covered the whole brain (please see attached). I used the following commands: mris_preproc --fsgd 3gps_IQ.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.3gps_IQ.thickness.10.mgh mri_glmfit --y lh.3gps_IQ.thickness.10.mgh --fsgd 3gps_IQ.fsgd doss --C 3gps_IQ_Ftest.mtx --C 3gps_IQ_AbusedmorethanHC.mtx --C 3gps_IQ_AbusedmorethanPC.mtx --C 3gps_IQ_PCmorethanHC.mtx --surf fsaverage lh --cortex --glmdir lh.3gps_IQ_thickness mri_glmfit-sim --glmdir lh.3gps_IQ_thickness --cache 2 abs --cwp 0.05 --2spaces F contrast: 1 -1 0 0 0 0 -1 0 What went wrong? Please kindly help... Many thanks, Lena -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: 04 August 2015 19:52 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] contrasts The F would be 1 -1 0 0 0 0 -1 0 Your t-contrasts are correct (you don't need to do both directions) On 08/03/2015 03:40 PM, Lim, Lena wrote: Hi experts, I have 3 groups: (A, PC and HC) and 1 covariate: IQ. For a DOSS file, how should I define the F contrast? Would it still be: I -1 0 ? 1 0 -1 And would the t contrast for say APC be: 1 -1 0 0 and for A PC be -1 1 0 0 etc Many thanks, Lena ___ 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. # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2015/08/14-14:59:29-GMT # cmdline mri_surfcluster --in lh.3gps_IQ_thickness/3gps_IQ_Ftest/sig.mgh --csd /software/system/freesurfer/freesurfer-5.3.0//average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/abs/th20/mc-z.csd --mask lh.3gps_IQ_thickness/mask.mgh --cwsig lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.cluster.mgh --vwsig lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.voxel.mgh --sum lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.cluster.summary --ocn lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.ocn.mgh --oannot lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.ocn.annot --annot aparc --csdpdf lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.pdf.dat --cwpvalthresh 0.05 --o lh.3gps_IQ_thickness/3gps_IQ_Ftest/cache.th20.abs.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white # cwd /home/spjwker_PAC/Lena/CT_SA/FSL # sysname Linux # hostname nanlnx1.iop.kcl.ac.uk # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input lh.3gps_IQ_thickness/3gps_IQ_Ftest/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # annot aparc # SUBJECTS_DIR /home/spjwker_PAC/Lena/CT_SA/FSL # SearchSpace_mm2 65416.6 # SearchSpace_vtx 149953 # Bonferroni 2 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold0 mm^2 # CSD thresh 2.00 # CSD nreps1 # CSD simtype null-z # CSD contrast NA # CSD confint 90.00 # Overall max 23.1633 at vertex 102919 # Overall min 0 at vertex 8 # NClusters 1 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow CWPHi NVtxs Annot 1 23.163 102919 76038.98-35.47.0 -9.7 0.00020 0.0 0.00040 149021 insula ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this
Re: [Freesurfer] Freeview
Page up / down is moving the current slice up and down but it not flipping between the slices ?! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias Sent: Wednesday, August 19, 2015 12:21 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview Page up / page down should work Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:16:13 PM Subject: [Freesurfer] Freeview Hi Freesurfers, I can’t change the current slice in freeview using the Up or Down key as described in the Freesurfer wiki. Instead the Up/Down key are moving the current slice up or down and not changing the current slice. Is there any shortcut that can change the current slice instead of the Up/ Down keys Thanks Mohamad ___ 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
[Freesurfer] Freeview
Hi Freesurfers, I can't change the current slice in freeview using the Up or Down key as described in the Freesurfer wiki. Instead the Up/Down key are moving the current slice up or down and not changing the current slice. Is there any shortcut that can change the current slice instead of the Up/ Down keys Thanks Mohamad ___ 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] surface lines in manual edits
Hi, I'm hand editing brains to get the most accurate cortical thickness analysis possible, and ran into a bit of a problem with surface lines. One issue is with the original structural reconstructions from the hdr files, and the other deals with the manual edits I've made when the recon was re-run. 1. A couple of the volumes initially had the white matter surface as the pial surface/cortical surface. Initially I tried running g-cut for some of the suggestions I found on the wiki when the surface lines are off. This didn't work on those problem volumes. 2. When editing with control points in order to get the white matter areas that were not incorporated into the white matter surface included, the control points have overcoverected and made the same issue that was the occurrence with the two or three original volumes - the white matter surface is seen as the brain/pial surface. I was conservative with these as well. I have been looking on the wiki for a way to adjust the actual surface lines manually based on the actual white matter/brain surface. I think this would be most useful, but I'm not sure if it is possible. If so, how could this be done - and, if not, what possible way of trouble shooting can help deal with this white matter as pial surface issue? Best regards, - Jennifer Lynn Sarai Kriegel MS in Psychological Sciences, Cognition and Neuroscience Emphasis Functional Neuroimaging of Memory Lab, Center for Vital Longevity The University of Texas at Dallas jlk130...@utdallas.edumailto:jlk130...@utdallas.edu I am looking for a lot of men who have an infinite capacity to not know what can't be done. - Henry Ford The important thing is not to stop questioning. Curiosity has its own reason for existing. - Albert Einstein ___ 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
Got it! Thanks Iglesias -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias Sent: Wednesday, August 19, 2015 12:38 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview Weird! The up and down arrows should move the current slice up and down, whereas page up/down should change the slice... You can also click on the other views to change the current slice. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:23:28 PM Subject: Re: [Freesurfer] Freeview Page up / down is moving the current slice up and down but it not flipping between the slices ?! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias Sent: Wednesday, August 19, 2015 12:21 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview Page up / page down should work Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:16:13 PM Subject: [Freesurfer] Freeview Hi Freesurfers, I can’t change the current slice in freeview using the Up or Down key as described in the Freesurfer wiki. Instead the Up/Down key are moving the current slice up or down and not changing the current slice. Is there any shortcut that can change the current slice instead of the Up/ Down keys Thanks Mohamad ___ 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 ___ 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
[Freesurfer] Surface-based Cluster Summary Table as created by mri_glmfit-sim
Hello Freesurfer's experts, I used the group analysis clusterwise correction with glmfit-sim and I found that Annot field in Cluster Summary Table don't always fit well with the corresponding region on ?h.aparc.a2009s.annot file. How is determined precisely each localization of each cluster in the summary table ? Thanks in advance ! Best regards, Matthieu ___ 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
Weird! The up and down arrows should move the current slice up and down, whereas page up/down should change the slice... You can also click on the other views to change the current slice. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:23:28 PM Subject: Re: [Freesurfer] Freeview Page up / down is moving the current slice up and down but it not flipping between the slices ?! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias Sent: Wednesday, August 19, 2015 12:21 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview Page up / page down should work Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:16:13 PM Subject: [Freesurfer] Freeview Hi Freesurfers, I can’t change the current slice in freeview using the Up or Down key as described in the Freesurfer wiki. Instead the Up/Down key are moving the current slice up or down and not changing the current slice. Is there any shortcut that can change the current slice instead of the Up/ Down keys Thanks Mohamad ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using FreeSurfer Suggested Morphometry Sequences
You can run this command to incorporate the T2 image: recon-all -i /path/to/MEMPRAGE -T2 /path/to/T2 -T2pial -s subject_name -all After completing, this will produce ?h.pial which use the T2 image, and ?h.woT2.pial which are the same pial surfaces as recon-all without T2 input. Best, Lee On Tue, 18 Aug 2015, Bruce Fischl wrote: no, there is a post-hoc recon-all target you can use. -T2 or -T2pial or something. Sorry, I don't remember, maybe someone else can fill in the details Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi Bruce, Thanks so much! We do have a bandwidth matched T2-space. So should that be fed into recon-all at the same time as the MEMPRAGE as a second series? best, John On 8/18/15, at Tue,Aug 18 - 8:32:00 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi John the MEFLASH never achieved as good cortical contrast as the memprage, so for cotical stuff we still recomment memprage. And yes, feeding the RMS to recon-all will be fine. If you can get a readout/bandwidth matched T2-space or FLAIR that can be a pretty big help as well for avoiding dura cheers Bruce On Tue, 18 Aug 2015, John Pyles wrote: Hi all, We have recently installed the FreeSurfer suggested morphometry sequences on our Siemens Verio 3T. Specifically, the multiecho MPRAGE (MEMPRAGE), and multiecho FLASH (MEFLASH). Our goal is to get the best FreeSurfer reconstruction results possible for use with fMRI surface analyses, diffusion imaging, and other purposes. For the current project, scan time is not at a premium since we have 60-90min budgeted for anatomical and diffusion weighted scans. We’re just looking for the best results. However, after looking through the wiki and email archives, I’m having a hard time figuring out what the most up to date recommendations are for what sequences to use and how to use them with recon-all. Some specific questions: 1) The original 2009 Suggested Morphometry Protocols” document, the MEFLASH seems to be recommended as the best sequence to use for whole-brain segmentation. But other more recent posts to the email list suggest using MEMPRAGE as the default protocol. We also have a very nice T2-SPACE protocol we’ve been running. What is the current recommendation? 2) Is the procedure for using MEMPRAGE with recon-all to just input the RMS scan and not the 4 different echos? 3) Is it possible to use the MEFLASH scans with recon-all? If so, how are they input and is processing of the two different echo time scans required before running recon-all? The wiki entry on MEF is from 2008, so I’m not sure what’s happened since then. 4) What is the current recommendation on using the -3T and -mprage flags with recon-all? 5) Since we are scanning on a Siemens Verio instead of the TIM Trio scanners I believe the sequences were developed on, we have had to modify some protocol parameters. If anyone has been successfully scanning MEFLASH and/or MEMPRAGE on a Verio or possibly Skyra and has good parameters to use that would be great. Our test scans look good, but there is always room for improvement. 6) Finally, is 1mm isovoxel still recommended? Or should we try to push the resolution below 1mm? Thanks so much in advance for any advice! best regards, John __ John Pyles, Ph.D. Research Scientist Center for the Neural Basis of Cognition Department of Psychology Carnegie Mellon University email: jpy...@cmu.edu phone: 206.552.0107 __ ___ 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 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,
Re: [Freesurfer] Trakula
Hi Bahram - There are some errors in there related to registration files. Can you please send these files? bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat Thanks, a.y On Tue, 18 Aug 2015, B M wrote: Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Could you please advise me what to do? Best Bahram ___ 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] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?
Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error: /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 35: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic link pointing to no existing file. I have similar problems when I try to run a T1T2 or a T2. Can someone help me with this issue? Thanks, Alex -- Alexandra De Araujo Adjunct research assistant Brain and memory lab University of Oregon (+1) 541-346-6733 -- ___ 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] FreeSurfer 6.0 dev version Output
Hi Prya,
that is because MriCron is not that great at overlaying images that are in the
same physical space but not in the same voxel space. You have two options here:
1. Use FreeSurfer's Freeview rather than MriCron to visualize the output.
FreeView will correctly overlay the segmentation.
2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
lh.hippoSfLabels-T1.v10.mgz) when you call mri_extract_label. That volume lives
in the same voxel space as T1.nii, and should be properly overlayed by MriCron.
However, the resolution of the segmentation will be 1 mm, rather than the 0.333
mm that you'd get in option 1.
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, August 19, 2015 7:50:12 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi
This is a follow-up question to my previous problem.
After I run recon-all -all -i ${subject}.nii -subject ${subject}
-hippocampal-subfields-T1, I extracted the left CA1 using mri_extract_label
lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the alignment is
not correct (see attached picture).
I wonder what is causing this issue? Since the CA1 was extracted from the same
T1 image, they should technically be in the same space and therefore should
align correctly.
Please advise.
Thank you,
Priyanka
On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta priyankamehta0...@gmail.com
wrote:
Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias e.igles...@bcbl.eu
wrote:
Hi again,
instead of:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
your can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
Cheers,
/E
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka Mehta priyankamehta0...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 11:26:04 AM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Thanks Eugenio! Thats worked!
One more question- how would I convert the lh.CA1.mgz that I get from the
previous step to .nii format?
Best,
Priyanka
On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias e.igles...@bcbl.eu wrote:
Hi Priyanka,
you can use mri_extract_label for that. For example, if you are interested in
CA1 (label 206), you can run:
mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
Cheers,
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Priyanka priyankamehta0...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, July 29, 2015 7:59:37 AM
Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi,
I am new to FreeSurfer and need help with hippocampal segmentation in the 6.0
dev version.
I used the following command: recon-all -i ${subject}.nii -subject ${subject}
-all -hippocampal-subfields-T1.
I can also view the segmented hippocampal regions using the command: freeview
-v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
However, is there a way I can get a separate .nii file for each of my
hippocampal subregion?
I would really appreciate any help in the matter.
Best,
Priyanka Mehta
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Re: [Freesurfer] visualizing paths stats by voxel
Hi Janosch - There is a bug in how the output paths are saved when longitudinal TRACULA is run with one time point only. I'm working on a fix. In the meantime, you can try your analysis with the subjects that have multiple time points and you won't be affected by this problem. I can see that the subjects with a single time point are about 1/3 of your sample, and so you may not want to drop them completely. Thank you for trying things that nobody else has tried and finding these bugs! More soon, a.y On Mon, 17 Aug 2015, Janosch Linkersdörfer wrote: Hey Anastasia, thanks for looking into this. Am 17.08.2015 um 20:33 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - Looking at the stats files of your subjects, just by a quick count of the number of lines, I see that there are some subjects that have only 1 time point and some that have multiple time points, and that the pathstats.byvoxel.txt files have different lengths between those two types of subjects. I suspect that the strange average path that you get has to do with how this mixing of subjects was done. Did you run the subjects with a single time point through the longitudinal stream as well? Yes, I ran the longitudinal stream for all subjects, also for the ones with only one time point. Thanks, Janosch Best, a.y On Sun, 9 Aug 2015, Janosch Linkersdörfer wrote: Hi Anastasia, yes, I am. But it looks similar in the distributed version :( Thanks, Janosch Am 08.08.2015 um 00:48 schrieb Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Janosch - Are you by any chance using the dev version of freeview? a.y On Fri, 7 Aug 2015, Janosch Linkersdörfer wrote: Hi Anastasia and list, I'm trying to do analyses along the tract with the path_stats_byvoxel files. When I am visualizing the points using the waypoint functionality of Freeview, it looks a little strange, i.e., the points are not equally spaces on the tract, but clumped together at some parts and spread out on others, see: this looks different to your slides: Also, the most posterior points seem to be strangely located (in the other hemisphere). What could be the reason for this strange behavior? Thanks, Janosch 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] cross and long in qdec
Hi, If I have a set of subjects from a study collected at time 0 (T0) and a subset of these subjects that also have data collected at time 1 (T1), can I run qdec on the T0 subject's with no T1 together with the longs of the subject's at T0 that have a T1? Thanks, P ___ 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] nu_correct flag for memprage
Hi, For memprage data collected on a 3T scanner could you please let me know what nu_correct flag should be used for recon-all? Should we use -nuintensitycor-3T? Thanks, P ___ 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.
