Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

Hippocampal Subsectioning
by Joshua S 13 Jul '14

13 Jul '14

Hi, I was doing a hippocampal subsectioning <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation> on a data set. Previously recon-all -all was used, and then I did recon-all -hippo-subfields. I then used the script kvlQuantifyHippocampalSubfieldSegmentations.sh to find the volume of the hippocampus and its sub parts. I was confused as to the data I was getting out. The hippocampus seems to large. The voxel size is 0.5 mm * 0.5 mm * 0.5 mm so the hippocampal areas seem to large. Also the subunits of the hippocampus are larger than the actual hippocampus which again does not make sense. I attached one of the output files Thank you for any replies, From Joshua Segaran

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Understanding Hippocampal volume stats
by Zia, Mohammad 13 Jul '14

13 Jul '14

Hi, Freesurfer reported the following hippocampal volumes for a subject volumeInVoxels: right_CA1: 2652.3 right_CA2_3: 7245.11 right_CA4_DG: 3967.28 right_fimbria: 423.555 right_hippocampal_fissure: 191.897 right_presubiculum: 3598.99 right_subiculum: 4868.1 Right-Hippocampus: 3258.77 I have two questions about it 1. I don’t understand why the right_subiculum volume is more than the Right-Hippocampus volume. 2. Since the voxel size for the volumes is 0.5^mm, do we have to divide these volumes by 8 to convert them to voxel size 1^mm so that we can do direct comparison with other freesurfer stats volume (for example the volumes in rh.aparc.stats)? Thanks --Mohammad Zia This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original.

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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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Freesurfer July 2014