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Re: [Freesurfer] Correlation coeffecient
by Lars M. Rimol 13 Jul '14

13 Jul '14

Hi Doug, A naive question in regard to the issue brought up by Chris (see below): Could one simply use this formula (with the F from the GLM for a given contrast): r² = F/(F+df) ? LMR try this oneftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_p… On 07/11/2014 01:51 PM, Chris Wertz wrote: > Hi Freesurfer experts > > I am trying to obtain correlation coefficients for significant > clusters and found a previous post about this, > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023616.html > > > but the MATLAB function link within this post is dead? > > any help is greatly appreciated > > thanks, > Chris -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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Re: [Freesurfer] create label from binary .mgh file {Disarmed}
by Lars M. Rimol 12 Jul '14

12 Jul '14

Hi Doug, That works! Thanks! I don't know why it didn't the first time (I can't find the old command line). But this command line works (in case anybody else wants to do the same thing): [LMR in ~ ] mri_cor2label --i /home/lmr/ANALYSIS/binary_pmaps/lh_binarymap_area_covar8.mgh --id 1 --l /home/lmr/ANALYSIS/binary_pmaps/lh_binarymap_area_covar8 --surf fsaverage lh LMR Douglas N Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Fri, 11 Jul 2014 11:02:38 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> use mri_cor2label with the --surf option On 07/11/2014 01:36 PM, Bruce Fischl wrote: > Hi Lars > > this would be pretty simple to do in matlab, but I'm not sure if we > have anything do to it otherwise (Doug might) > > cheers > Bruce > On Fri, 11 Jul 2014, Lars M. Rimol wrote: > >> Hi, >> >> Is there a way to take a binary .mgh file (surface file with 163842 >> vertices containing 1 or >> 0) and create a label such that the ones in the input file == the >> label? For instance, to >> create a label from a p-map. >> >> I tried using mri_cor2label based on previous responses on the >> mailing list, but that seems >> to produce volumes and I'm not really sure what it does anyway... >> >> >> Thank you! >> >> >> >> -- >> yours, >> Lars M. Rimol, PhD >> St. Olavs Hospital >> Trondheim, >> Norway >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)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/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. - Previous message <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36914.html> - View by thread <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/index.html#36917> - View by date <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/maillist.html#36…> - Next message <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36915.html> - [Freesurfer] create label from binary .mgh file <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36913.html> Lars M. Rimol - - Re: [Freesurfer] create label from binary .mgh file <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36914.html> Bruce Fischl - - Re: [Freesurfer] create label from binary .mgh fi... Douglas N Greve Reply via email to [image: The Mail Archive] <http://www.mail-archive.com/> - The Mail Archive home <http://www.mail-archive.com/> - freesurfer - all messages <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/> - freesurfer - about the list <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/info.html> - Previous message <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36914.html> - Next message <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36915.html> -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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Segmentation fault with mri_ca_train
by Mark Plantz 11 Jul '14

11 Jul '14

Hello freesurfers, I am running into some sort of memory allocation issue when running mri_ca_train. I am simply using an intensity volume and a segmentation volume to create a GCA atlas. I keep getting this "segmentation fault: 11", which is data allocation error. I have tried using all different environments and can't avoid it. The output is below: sh-3.2# mri_ca_train -T1 withSkull.mgz -seg seg_edited.mgz atlas_test /hearingbrain/Desktop/atlas_withSkull.gca reading T1 data from subject's mri/withSkull.mgz directory reading segmentation from subject's mri/seg_edited.mgz directory training on 1 subject and writing results to /Volumes/Macintosh HD/Users/hearingbrain/Desktop/atlas_withSkull.gca *************************************************************************** processing subject atlas_test, 1 of 1... reading input 0: /Applications/freesurfer/subjects/atlas_test/mri/withSkull.mgz gca width modified from 256 to 181 gca height modified from 256 to 217 gca depth modified from 256 to 181 Segmentation fault: 11 Any ideas? -MP

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[FreeSurfer] Importing DICOM Files
by Matthew Clem 11 Jul '14

11 Jul '14

Hi FreeSurfers, I am very new to FreeSurfer and I'm having some issues uploading my first subject. I have a subject folder with 160 .dcm files and FreeSurfer cannot find the files. Here is the script I used: recon-all -s 0000142 \ -i $SUBJECTS_DIR/0000142/000001.dcm I even tried to type out the full path instead of using $SUBJECTS_DIR variable and cd to where the files are stored and it still didn't work. Here is my output: ERROR: cannot find /home/mclem/freesurfer/testsubjects/0000142/000001.dcm Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0000142 exited with ERRORS at Fri Jul 11 15:27:34 CDT 2014 Any thoughts on what I'm doing wrong? Thanks, Matthew Clem, M.Ed. Doctoral Student Clinical Psychology UT Southwestern Medical Center Matthew.Clem(a)utsouthwestern.edu<mailto:tabatha.melton@utsouthwestern.edu> ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Tutorial Installation Issue
by Kundrod, Kathryn (NIH/NIBIB) [F] 11 Jul '14

11 Jul '14

Hi all, I have a question regarding the installation of the buckner tutorial dataset. I have been able to download and unzip the tutorial data, but it seems only partially downloaded. In the readme, I see that there are supposed to be 3 subfolders to the dataset: group_study, tutorial_subjs, and raw, but my download only contains one subfolder (tutorial_subjs). I have tried downloading multiple times in multiple ways without a change in results. Is anyone aware of what might be causing this? Thank you! Kathryn Kundrod

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exporting movies from freeview
by pavitrak＠nmr.mgh.harvard.edu 11 Jul '14

11 Jul '14

Hi Freesurfer Team, I have a 4D volume mask of MRI mask values over time - which I can view frame by frame within Freeview. Is there any way to export this in movie form out of freeview so I can play it back independently of the interface? Thank you. Best Regards, Pavitra

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Correlation coeffecient
by Chris Wertz 11 Jul '14

11 Jul '14

Hi Freesurfer experts I am trying to obtain correlation coefficients for significant clusters and found a previous post about this, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023616.html but the MATLAB function link within this post is dead? any help is greatly appreciated thanks, Chris

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create label from binary .mgh file
by Lars M. Rimol 11 Jul '14

11 Jul '14

Hi, Is there a way to take a binary .mgh file (surface file with 163842 vertices containing 1 or 0) and create a label such that the ones in the input file == the label? For instance, to create a label from a p-map. I tried using mri_cor2label based on previous responses on the mailing list, but that seems to produce volumes and I'm not really sure what it does anyway... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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Creating own atlas
by Brianna Damadian 11 Jul '14

11 Jul '14

Hello, I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? Thanks, Brianna

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Anterior Temporal Lobe / Pial Reconstruction Troubles - part 2
by Las Blawimo 11 Jul '14

11 Jul '14

Attached you will find image 3 and 4. Sincerely, Las

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