Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

mri_convert generates different mgz from nii and nii.gz
by Forrest Sheng Bao 16 Aug '11

16 Aug '11

hi there, i noticed a strange problem tonight. I had a .nii.gz file. I used mri_convert to convert it into a .mgz file. I also used gzip to unzip the .nii.gz file and then used mri_convert again to get another .mgz file. But the two .mgz files have different md5 sums. Does anyone know what caused the problem? Or is there a problem? Cheers, Forrest

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Abnormal segmentation of hippocampal subfields
by New Fei Ho 16 Aug '11

16 Aug '11

Hi, I've been inspecting the hippocampal subfield segmentation in my subjects. So far, the subfields segmentation appear to be consistent across my images. 1. Is there any criterion used in defining proper subfield segmentation (any landmarks I should look out during QC)? 2. What are the corrective measures when the subfield segmentation fails? I attach examples of 2 subjects that have two T1-weighted scans taken in tandem in the same session (of which one two images appears to have malfunctioned segmentation) Thanks, Newfei

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Saving annotation and stats after expand boundary of region
by Keefe, Helen L 16 Aug '11

16 Aug '11

Hi Bruce, Doug, and All, I have corrected a boundary between lh corpuscallosum and caudalanteriorcingulate. I have overwritten the label/lh.aparc.annot as per Bruce's email below. However, doesn't this leave a number of files with incorrect information now in the stats directory? Do I need to rerun something to bring these up to date? Thanks, Helen ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Monday, July 11, 2011 2:57 PM To: Keefe, Helen L Subject: RE: [Freesurfer] save label after expand boundary of region sure. Good luck Bruce On Mon, 11 Jul 2011, Keefe, Helen L wrote: > Thank you! > > This will help me clear up a lot of problem scans - I really appreciate your help > > Helen > > > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Monday, July 11, 2011 2:42 PM > To: Keefe, Helen L > Subject: RE: [Freesurfer] save label after expand boundary of region > > no, it won't matter > On Mon, 11 Jul 2011, Keefe, Helen L wrote: > >> Hi Bruce - >> >> I made the edits on the pial surface using command: >> >> >> tksurfer $i lh pial -annotation aparc >> >> >> Does that make any difference? Since the instructions say to use the inflated surface: >> >> tksurfer -annot aparc subjectid rh inflated >> >> Thanks, >> Helen >> >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Monday, July 11, 2011 11:31 AM >> To: Keefe, Helen L >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] save label after expand boundary of region >> >> if you export it as an annotation then all the labels will be combined in >> one file. I think you are probably editing the ?h.aparc.annot, so you could >> overwrite that one if you want. The correct mri_segstats command could then >> be found in the subject's recon-all.log or recon-all.cmd file in the >> scripts dir. >> >> cheers >> Bruce >> >> >> On Mon, 11 Jul 2011, Keefe, Helen L wrote: >> >>> Hi Bruce, Doug, and All: >>> >>> Questions on a continuing problem: >>> >>> When I run tksurfer, the caudalanteriorcingulate is invaded by the corpuscallosum. >>> I edited the boundary using the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit >>> >>> I'm then instructed to "Save the annotation: File > Label > Export Annotation. Probably choose a new name rather than writing over an existing file" >>> >>> I don't need a new name - I just need to save the labels for the caudalanteriorcingulate and the corpuscallosum, which both now look correct. How/where >>> do I do that? Here are the files in the label dir: >>> >>> lh.cortex.label >>> lh.aparc.annot >>> lh.aparc.a2009s.annot >>> rh.cortex.label >>> rh.aparc.annot >>> aparc.annot.ctab >>> rh.aparc.a2009s.annot >>> aparc.annot.a2009s.ctab >>> >>> >>> Also - >>> >>> I previously asked what I need to do after that to ensure accurate measurements. >>> Bruce responded, >>> "I don't think you need recon2 since you are just changing the aparc. I believe you can just run the aparc stats step, but I'll cc Doug who might know >>> better." >>> >>> Any advice on all this? >>> >>> Thanks, >>> Helen >>> >>> >>> __________________________________________________________________________________________________________________________________________________________ >>> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential >>> and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying >>> of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. >>> >>> __________________________________________________________________________________________________________________________________________________________ >>> >>> >> >> >> 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. >> >> >> ________________________________ >> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. >> ________________________________ >> >> >> > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. > ________________________________ > > > ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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automated brodmann parcellation
by Corey Keller 16 Aug '11

16 Aug '11

Hi Freesurfers, I was wondering if you have come across a method to automatically parcellate the whole brain into Brodmann areas. I know the newest freesurfer version does this for several BAs but not all BAs have been incorporated. I was wondering if anyone knows of an existing Brodmann atlas (for example from Micron, AFNI, FSL, WFU_PickAtlas) that I can download and apply to my subjects' surfaces in freesurfer via mri_vol2surf? Thanks in advance. Best, Corey

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Re: [Freesurfer] QDEC - generate stats data table error: cannot find /usr/local
by Jamaan Alghamdi 16 Aug '11

16 Aug '11

Hi Rajeev, Usually, this type of error is produced if stats file is missed, check if aseg. stats file is there in directory "/usr/local/freesurfer/subjects/140/stats" directory. If this file is missed in some subjects, you can add "--skip" to command line like; asegstats2table --subjects 01 02 03 .... --meas volume --skip --statsfile wmparc.stats --all-segs --tablefile ....... Jamaan Jamaan Alghamdi 07779801950 0151 795 4627 Magnetic Resonance & Image Analysis Research Centre (MARIARC) University of Liverpool Pembroke place Liverpool L69 3GE http://web.mac.com/jamaan/Jamaan/Welcome.html http://www.easyneuroimaging.com/

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Intracranial volume
by carolina.mr 16 Aug '11

16 Aug '11

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preproc-sess - cannot find AFNI command 3dvolreg
by Adam Nitenson 16 Aug '11

16 Aug '11

Hi Doug and Freesurfers, I encountered an error during preproc-sess (Stable 5) that I have never seen before: ERROR: cannot find AFNI command 3dvolreg The commands I entered were: setenv USE_STABLE_5_0_0 source /usr/local/freesurfer/nmr-stable50-env setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd $SUBJECTS_DIR preproc-sess -s MTH20100AA -fwhm 5 -per-run I've run this set of commands many times without this problem, so did something change or am I missing something simple? Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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volumes 2
by carolina.mr 16 Aug '11

16 Aug '11

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Large White Matter Areas Ignored In Surface Detection
by Christopher Luna 16 Aug '11

16 Aug '11

Hello Freesurfers, I'm putting *.IMG files into the program and after correcting talaraich transformations for them, I notice that when the reconstructions have completed, that there are entire lobes of white matter absent from the surfaces detected and from the wm.mgz file. I went through my hand at first to manually fill in the missing white matter for the first case, but after seeing how many were affected, I figured there was some setting I may be missing or some contrast level that may be off. I had tried using control points, but after following the WIKI instructions on regenerating surfaces after placing them, I found no significant difference in white matter detection. How do I ensure all of the white matter in my converted IMGs is identified? Thank you kindly, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT

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QDEC - generate stats data table error: cannot find /usr/local
by rajeev krishnadas 16 Aug '11

16 Aug '11

Hi all, I am new to this, and wonder if you could help me set this up please. OS: Ubuntu 10.10 ; 64 bit (a complete newbie with linux) I am going through buckner - tutorial for the group analysis with Qdec. I am at the step where I have to import the aseg and aparc data. I clicked on the "generate stats data tables" button - unfortunately an error showed up "again". ---------------------------------------------------------------------------------------------------------------------------------------------------------------- krishnadas-desktop:/usr/local/freesurfer> mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ ---------------------------------------------------------- asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 140 049 141 084 021 093 080 091 040 017 138 106 108 092 124 129 103 130 039 123 095 067 004 133 097 073 149 045 136 144 032 131 145 111 102 074 114 008 128 099 /usr/local/freesurfer/bin/asegstats2table:5: DeprecationWarning: the sets module is deprecated from sets import Set Building the table.. SUBJECTS_DIR : /usr/local/freesurfer/subjects ERROR: cannot find /usr/local/freesurfer/subjects/140/stats/aseg.stats Use --skip flag if you want to continue in such cases ---------------------------------------------------------------------------------------------------------------------------------------------------------------- The path seems to be right, and the files seems to be there!!! I am doing something wrong, but cannot understand what!!!! Thanks in advance. Cheers Rajeev -- Dr Rajeev Krishnadas MBBS, MD, DipNB, MRCPsych|Clinical Lecturer in Psychological Medicine|Sackler Institute of Psychobiological Research|Southern General Hospital|Glasgow|G51 4TF|T: +44(0)141 232 7699|F: +44(0)141 232 7697|M: +44(0)7525343479 http://etanerceptforpsoriasis.moonfruit.com/#/home/4545962633 | Hasta la victoria siempre |

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Freesurfer August 2011