Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

Installation difficulties (Mac)
by Julia Nantes 16 Oct '12

16 Oct '12

I have downloaded the FreeSurfer software onto a Mac computer. I did the setenv/source steps and got this output: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/ FSFAST_HOME /Applications/freesurfer//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer//subjects MNI_DIR /Applications/freesurfer//mni Next, I obtained a license and finally got the text to go into a pico .license file after doing this: [Lisa-Koskis-iMac:~] rsussex% sudo -s Password: [Lisa-Koskis-iMac:~] root# cd /Applications/freesurfer/ [Lisa-Koskis-iMac:/Applications/freesurfer] root# pico $FREESURFER_HOME .license FREESURFER_HOME: Undefined variable. [Lisa-Koskis-iMac:/Applications/freesurfer] root# pico .license [Lisa-Koskis-iMac:/Applications/freesurfer] root# ls ASegStatsLUT.txt SetUpFreeSurfer.sh fsfast AUTHORS Simple_surface_labels2009.txt lib DefectLUT.txt VERSION matlab FreeSurferColorLUT.txt WMParcStatsLUT.txt mni FreeSurferEnv.csh average sessions FreeSurferEnv.sh bin subjects LICENSE build-stamp.txt tkmeditParcColorsCMA NOTICE data tktools README diffusion trctrain SegmentNoLUT.txt docs SetUpFreeSurfer.csh fsafd [Lisa-Koskis-iMac:/Applications/freesurfer] root# cd ../.. [Lisa-Koskis-iMac:/] root# cd /Applications/freesurfer//subjects/ [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# ls README bert fsaverage fsaverage4 fsaverage6 rh.EC_average sample-002.mgz V1_average cvs_avg35 fsaverage3 fsaverage5 lh.EC_average sample-001.mgz [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# tkmedit bert orig.mgz tkmedit: Command not found. [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# qdec qdec: Command not found. Since the 'Testing your FreeSurfer installation" commands from the wiki page are not working, I may not have installed this properly. Any insights as to how this could be resolved would be much appreciated. Thank you, Julia

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Re: [Freesurfer] error measuring LGI
by Gabriel Gonzalez Escamilla 16 Oct '12

16 Oct '12

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3 Factor glm group analysis
by hhal5293＠uni.sydney.edu.au 16 Oct '12

16 Oct '12

Hello, We are currently doing a longitudinal Group Analysis using FreeSurfer, and were wondering if there is a way to run a 3 factor design (time is 2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do this using mri_glmfit, is it possible to do this using QDEC? Regards, Harry

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pctsurfcon question
by Phil Greer 16 Oct '12

16 Oct '12

I do not have a question on how to use the program, the wiki covered that well. My question is about the formula embedded in the program to calculate the contrast. The formula is ((wm-gm)/((wm+gm)/2))*100 This creates a dynamic range of -200 to +200. Which the last time I checked is not really a percent as the command name implies. Was there some reasoning behind this that I am missing? Phil Greer University of Pittsburgh

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error measuring LGI
by Gabriel Gonzalez Escamilla 16 Oct '12

16 Oct '12

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Can I get verification of some scripts I wrote to parallelize recon-all?
by Chris Adamson 15 Oct '12

15 Oct '12

Hey all, Can I send through some shell scripts that I wrote to run all the hemisphere-specific steps so that the lh and rh steps are run together. If I could send them through to make sure I'm doing autorecon2-wm and autorecon3-pial correctly? Thank you. Chris. -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental Imaging, Critical Care and Neurosciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 9906 6780 M XXXX XXX XXX E chris.adamson(a)mcri.edu.au www.mcri.edu.au ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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mistake in webpage SubCortGray description??
by Fernando Ventrice 15 Oct '12

15 Oct '12

Dear all, I think in the following webpage there is a very small mistake: http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats It states that SubCortGray is the sum of the thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens, and VentralDC from both hemispheres. But I think SubCortGray sums all those areas plus the Cerebellum-Cortex from both hemispheres and the Brain-Stem. Please tell me if this is correct. Best, Fernando Ventrice El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar

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QA_tools missing signal to noise calculation
by Knut J Bjuland 15 Oct '12

15 Oct '12

Hi, I have downloaded the latest QA_tools v1.1 from http://surfer.nmr.mgh.harvard.edu/fswiki/QATools. However, when I ran recon_checker, I did not get a signal to noise calculations. I ran recon_checker with -s-dir subjectfile and -snaps-detailed. Is there any option that I missed? Is it possible to download a newer version from cvs? Knut J

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Lobe measures
by Mahinda Yogarajah 15 Oct '12

15 Oct '12

Dear Experts, I apologise for the repost but I was wondering if anyone could guide me with respect to deriving lobar measures and whether the commands below are correct . Thanks. M GM Lobar Values (1) mri_annotation2label --subject subject1 --hemi ?h --lobesStrict lobesfile (2) mri_anatomical_stats –mgz –cortex ../label/?h.cortex.label –f ../stats/?h.lobesfiles.stats –b –a ../label/?h.lobesfile.annot subject1 ?h white Q: Is this valid? Q:Do I need to include that part of the command in italics (-cortex...?hcortex.label) - is it not redundant given the use of the ?h.lobesfile.annot - using one or the other does give a different result at the top of the stats file (namely NumVert, WhiteSurfArea, and mean thickness which disappears if ?h.cortex.label is not passed) - why is this ? WM Lobar Values (1) mri_annotation2label --subject subject1 –hemi ?h --lobesStrict lobesfile (2) mri_aparc2seg --s subject1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.lobar.mgz --ctxseg aparc+aseg.mgz --annot ?h.lobesfile.annot Q: Is this valid ? Q: Do I need all the items in italics (hypo...rip...volmask) - they are present in the recon-all logfile but not in some forum posts on similar topics. (3a) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolourtable --etiv OR (3b) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/norm.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --ctab newcolourtable --etiv Q: Which of these should I be using - the latter is based on the recon-all log file, while the former is based on forum posts - what are the differences. Thanks. Mahinda

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Question about inferior temporal lobe topological/control points anomalies
by pietro de rossi 15 Oct '12

15 Oct '12

Dear FreeSurfer users and developers, I'm getting very frequently some bilateral inferior temporal lobe topological/control points anomalies. I attach an example with and without segmentation on. It seems to me that they are not affecting the pial surface's shape (inferior aspect of right temporal lobe attached in first picture. Should I edit and rerun recon? Thank you very much Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Freesurfer October 2012