Freesurfer

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30132 discussions

mri_vol2vol
by Andrew Bock 02 Oct '12

02 Oct '12

Hello, I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html When I run xhemireg I receive the error "ERROR: Option --keep-precision unknown" I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions? Andrew

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error in mri_segstats, important
by Knut J Bjuland 02 Oct '12

02 Oct '12

I have download the latest verion of mri_segstats from the release notes. But it does not generate asegstats. 4 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# ASeg Stats Tue Oct 2 07:36:17 CEST 2012 /home/knutjb/freesurfer/20_ucsd_automatic_version2/004 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject 004 ERROR: Option --sum unknown #------------------------------------------ recon-all -s 004 finished without error at Tue Oct 2 07:36:17 CEST 2012 done knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats USAGE: mri_label2vol Possible inputs: --label labelid <--label labelid> --annot annotfile : surface annotation file --seg segpath : segmentation --aparc+aseg : use aparc+aseg.mgz in subjectdir as seg --temp tempvolid : output template volume --reg regmat : VolXYZ = R*LabelXYZ --regheader volid : label template volume (needed with --label or --annot) for --seg, use the segmentation volume --identity : set R=I --invertmtx : Invert the registration matrix --fillthresh thresh : between 0 and 1 (def 0) --labvoxvol voxvol : volume of each label point (def 1mm3) --proj type start stop delta --subject subjectid : needed with --proj or --annot --hemi hemi : needed with --proj or --annot --surf surface : use surface instead of white --o volid : output volume --hits hitvolid : each frame is nhits for a label --label-stat statvol : map the label stats field into the vol --stat-thresh thresh : only use label point where stat > thresh --offset k : add k to segmentation numbers (good when 0 should not be ignored) --native-vox2ras : use native vox2ras xform instead of tkregister-style --version : print version and exit --help $Id: mri_label2vol.c,v 1.39 2012/06/08 17:29:54 greve Exp $ knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats --sum ERROR: Option --sum unknown Knut J

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Re: [Freesurfer] correcting rippled image
by Deirdre O Shea 02 Oct '12

02 Oct '12

Sorry, I thought I had attached the image. Here it is anyway. cheers, On Tue, Oct 2, 2012 at 3:08 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > I don't know since I don't know what went wrong. Send us an image and cc > the list and we'll take a look. > > > cheers > Bruce > On Tue, 2 Oct 2012, Deirdre O Shea wrote: > > Hi Bruce, >> >> That's what I meant so I take it that there's nothing i can do to improve >> the image with FreeSurfer then? >> >> Thanks, >> Deirdre >> >> >> >> On Tue, Oct 2, 2012 at 3:04 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Deirdre >> >> I'm not sure exactly what you mean, but probably what you are >> seeing (the circular patterns) are the effects of >> motion >> >> cheers >> Bruce >> On Tue, 2 Oct 2012, Deirdre O Shea wrote: >> >> Hey everyone, >> >> I was wondering if anyone knew how to correct for a ripple >> like effect in >> the image. I have adjusted the talairach and it still looks >> the same. Any >> suggestions would be great. see image attached. >> >> Thanks, >> Deirdre >> >> >> >> >> 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<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. >> >> >> >> >>

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correcting rippled image
by Deirdre O Shea 02 Oct '12

02 Oct '12

Hey everyone, I was wondering if anyone knew how to correct for a ripple like effect in the image. I have adjusted the talairach and it still looks the same. Any suggestions would be great. see image attached. Thanks, Deirdre

2 1

Appropriate Segmentation Sequence?
by Sullivan, Patrick M. 02 Oct '12

02 Oct '12

Hello, I have a set of archival data (so I was unfortunately not able to specify the acquisition sequences and include the recommended MPRAGE sequence). I am asking which sequence (if any) would be most conducive to volumetric/regional analysis using FreeSurfer. A Philips Achieva 3.0T was used for all acquisitions. All patients all have a the following sequences: FLAIR (TE 140ms, TR 10ms, Flip 90) T2W_FFE (TE 16ms, TR 1.5s Flip 18) Spin Echo (TE 16ms, TR 600ms Flip 90) DUAL_TSE CLEAR (TE 13ms, TR 3.4s, Flip 90) Would any of these be appropriate for segmentation and volumetric analysis? Thank you very much. -Patrick

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processing scans on more than one computer
by pietro de rossi 02 Oct '12

02 Oct '12

Dear FreeSurfer experts, I'm processing scans on three different computers and I would like to know if it is possible to collect all the processed scans together in order to analyze data on just one computer. I realized that even moving the processed subjects folders to another folder within the same computer (even if I set the new folder as the SUBJECTS_DIR) I'm not able to run tksurfer and tkmedit for those subjects....am I doing anything wrong? is it just that once you've processed the scans the proc_folders cannot be moved? thanks, 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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Average Thickness in QDEC
by Antonella Kis 02 Oct '12

02 Oct '12

Dear Experts, What is the best way to get the average thickness for each subject in QDEC, more exactly for the uncorrected clusters? I know when running QDEC theer is a stats_tables file saved so I wonder if the lh. aparc.thickness.stas.dat represents the mean cortical thickness. Should this values be the same with my thickness values under cache.th20.abs.y.ocn.dat obtained by running the mri_glmfit-sim with the option --cache where in order to catch all the clusters since I need the uncorrected one I used --cwpvalthresh .999? Thank you for you time and clarifications. Best regards, Antonella

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Lesioned brain (surface) registration to fs average
by octavian lie 02 Oct '12

02 Oct '12

Dear all, I need to mark the cortical extent of a lesion (intersection of the lesion and pial surface, where "lesion" represent a epilepsy related resection). After the pial labeling of the resection, I need to register the labeled surface to the fsaverage. I completed recon-all routine on the postop T1, and went nicely, corrected pial surface in a few places. Question: what is the best way to mark the pial extent of a resection? Is there a way to accurately register the lesioned pia to the fsaverage, potentially by masking the resection ROI? Thank you for your insight, Octavian.

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ADC map negative values
by Efrat Kliper 01 Oct '12

01 Oct '12

Dear FreeSurfers Users, When i am using the dt_recon function to create adc map i get quite a lot negative values, dose anyone encounter this problem? Thanks, Efrat

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random effects analysis with performance values
by Maryam Vaziri Pashkam 01 Oct '12

01 Oct '12

Hi Dough, I have run a searchlight analysis on 10 subjects and want to run a random effects analysis with mri_glmfit across subject. I have the results of each subject projected on the fsaverage surface. But I have no idea how to make it to 1) compare the values in each voxel with 0.5 instead of 0 2) how to make it ignore the fact that I dont have variance for each subject and only have a single performance value (support vector machine performance) for each voxel (it looks like the mri_glmfit needs a ces.var.nii) Any idea how I can do this? Sorry if this is a rookie question. I am totally new to searchlight and random effects analysis in fsfast. Thanks, Maryam

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