Freesurfer June 2007

freesurfer@nmr.mgh.harvard.edu

59 participants
82 discussions

F-Test and directed contrasts
by Juergen Haenggi 07 Jun '07

07 Jun '07

Dear Freesurfer users We have done a cortical thickness group comparison, but we are not absolutely sure which color corresponds to which contrast. In our *.mat file we specified -1 1 0 0 0 0, but the sig.mgh file shows both directed contrasts (group1 > group2 and group1 < group2). Where can we look which color corresponds to which contrast? We searched for the answer in the archives, but did not find it! Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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w file to label
by Robert Levy 07 Jun '07

07 Jun '07

Hello, I am trying to convert a w file into a label file, and the best way I came up with seems like it is too complicated to be the actual best way. What I am doing below is reading a list of subjects, and then for each subject, 1.) running mri_surfcluster, 2.) merging its output into a new label, and 3.) removing the component labels that went into it. # entered in bash shell # generate the .w file paint-sess -sf Subject_Lists/bw-group-error-5 -analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh # merge labels cat Subject_Lists/bw-group-error-5 | while read subject; do mri_surfcluster --in $subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-lh.w --thmin 0.5 --sign pos --subject $subject --hemi lh --surf orig --annot aparc --minarea 1 --sum $subject/bold/EMerror/rACC_lh_pos_0_ASce68/mask-0-h-label.sum --olab $subject/label/rACC_lh_pos_0_ASce68 ; cd $subject/label; mri_mergelabels $(ls rACC_lh_pos_0_ASce68*.label | sed 's/rACC/\-i rACC/g') -o rACC_lh_pos_0_ASce68.label; rm rACC_lh_pos_0_ASce68-0*.label; cd $SUBJECTS_DIR; done #check in tksurfer surf-sess -s mano001 -analysis EMerror -contrast rACC_lh_pos_0_ASce68 -map mask -hemi lh -fthresh 1 It seems to work, but if there is a more direct way, it may be better just because there is potential room for error the way I am doing it. Thanks, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2656 Charlestown, MA 02129 email: levy(a)nmr.mgh.harvard.edu phone: 617-726-1908 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab

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Turn Off Verbose Output
by James Porter 07 Jun '07

07 Jun '07

Howdy- I didn't see any flags in the help files, but are there some 'hidden' commands I could use to attenuate the verbosity of reg-feat2anat and aseg2feat? Thanks, Jim Porter TRiCAM Lab Coordinator Elliott Hall N437 612.624.3892 www.psych.umn.edu/research/tricam <http://www.psych.umn.edu/research/tricam>

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mapping aseg.mgz to group FEAT analyses
by Eric Feczko 07 Jun '07

07 Jun '07

Hey, I noticed on the freesurfer wiki a workflow for registering an individual's subcortical segmentation(aseg.mgz) to individual feat sessions using aseg2feat. Are there any scripts for registering an individual's subcortical segmentation to a group feat session (.gfeat directory)? -Eric

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Re: [Freesurfer] reg- feat2anat error
by Furlong, Carolyn 06 Jun '07

06 Jun '07

Hi niiRead(): unsupported timing pattern in Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz sorry for the delay, Best wishes Carolyn can you send the log file? Furlong, Carolyn wrote: Hi, When I try to register my functional data to anatomical data using reg-feat2anat --feat feat_directory --subject subject_name I get the following error message ERROR: could not read ///example_func.nii.gz as 24 What does this mean? And how can I fix this? Best wishes Carolyn ________________________________ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://owa.liv.ac.uk/exchweb/bin/redir.asp?URL=https://mail.nmr.mgh.harvar…> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Cortical ROIs analysis
by jorge luis 06 Jun '07

06 Jun '07

Hello all I have a question: How to threshold a thickness statistical parametric map by using FDR just in one specific label of the fsaverage cortical surface parcelation? In advance thank you a lot Jorge ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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mri_surfcluster problem
by Emily Cooper 06 Jun '07

06 Jun '07

hi, i am having a strange problem with mri_surfcluster. i give it the following command line: mri_surfcluster --in /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh --subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos --minarea 6 --sum /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.clusters/2.ccf.pos.output.sum.txt and i get this result in the summary: # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.26.2.4 2006/07/13 17:50:28 greve Exp $ # $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ # CreationTime 2007/06/01-19:04:15-GMT # cmdline mri_surfcluster --in /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh --subject fsaverage --hemi lh --thmin 0.5 --thmax 1.0 --sign pos --minarea 6 --sum /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.clusters/2.ccf.pos.output.sum.txt # cwd /disks/gpfs/fmri/emily.permutations/correlation.permutations # sysname Linux # hostname andrew.bsd.uchicago.edu # machine i686 # FixVertexAreaFlag = 1 # # Input /disks/gpfs/fmri/emily.permutations/correlation.permutations/perm.mghs/2.lh.ccf.perm.smooth6.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /home/ecooper/subjects # Minimum Threshold 0.5 # Maximum Threshold 1 # Threshold Sign pos # AdjustThreshWhenOneTail 1 # Area Threshold 6 mm^2 # Overall max 0.632052 at vertex 5494 # Overall min 0.12689 at vertex 750 # NClusters 2 # Total Cortical Surface Area 70394.7 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs 1 0.632 5494 85426.29 -50.2 -16.0 -7.2 161181 2 0.223 9300 23.61 -31.7 -26.7 9.9 68 the problem is that this is just entirely incorrect. when i view the input dataset in tksurfer, it's clear just from scanning over the vertices that 161181 out of 163842 total of them do not have intensity values between .5 and 1 (thmin and thmx), let alone in a giant cluster together. furthermore, when i make a historgram of a text file containing these intensity values, it shows that the majority of them are less than .5, and thus shouldn't be recognized as part of a cluster based on my specifications in the mri_surfcluster command: $breaks [1] -0.10 -0.05 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 [13] 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 $counts [1] 10 205 1320 3881 7834 12333 16777 20168 21369 20405 17219 13789 [13] 10453 7479 4897 2988 1599 737 283 81 14 1 $intensities [1] 0.0012206880 0.0250241086 0.1611308456 0.4737490997 0.9562871547 [6] 1.5054747867 2.0479486334 2.4618840102 2.6084886659 2.4908143211 [11] 2.1019030529 1.6832069921 1.2759854006 0.9129527227 0.5977710233 [16] 0.3647416413 0.1951880470 0.0899647221 0.0345454767 0.0098875746 [21] 0.0017089635 0.0001220688 $density [1] 0.0012206880 0.0250241086 0.1611308456 0.4737490997 0.9562871547 [6] 1.5054747867 2.0479486334 2.4618840102 2.6084886659 2.4908143211 [11] 2.1019030529 1.6832069921 1.2759854006 0.9129527227 0.5977710233 [16] 0.3647416413 0.1951880470 0.0899647221 0.0345454767 0.0098875746 [21] 0.0017089635 0.0001220688 $mids [1] -0.075 -0.025 0.025 0.075 0.125 0.175 0.225 0.275 0.325 0.375 [11] 0.425 0.475 0.525 0.575 0.625 0.675 0.725 0.775 0.825 0.875 [21] 0.925 0.975 any ideas as to what is going wrong here? am i using the thmin and thmax flags wrong? thanks so much, emily

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subcortical segmentation
by Mishkin Derakhshan 05 Jun '07

05 Jun '07

Hi, I am interested in just obtaining the subcortical segmentation labels and not generating surfaces. I would like to do this in as little time as possible and since I am only looking for label volumes (ie. hippocampal volumes) i figured that there must be some steps I can leave out of -autorecon2. Can anyone tell me the flags I should set to get the fastest way to generate these label files? I found: autorecon-all -subcortseg -subjid <subject> on the wiki, but it says this may take 11+ hours to complete so I thought I would just check before I batched things to run. many thanks, mishkin

5 9

scaling thickness values
by Goldman, Aaron (NIH/NIMH) [C] 05 Jun '07

05 Jun '07

Hi, regarding thickness analysis using Freesurfer data, I was wondering if it was recommended to use any kind of scaling (for example, to the subjects' overall average thickness). I'm interested regarding both node-by-node analysis using mris_glmfit, and region-based using the aparc.stats files. Thanks, -Aaron-

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Re: [Freesurfer] fmri conjunction/correlation map
by Cameron Ellis 05 Jun '07

05 Jun '07

Hi all, I have a few questions on two related topics. Topic 1, conjunction analysis: Thank you Doug for your response pointing out the mergecontrasts tool. I have 2 questions for anyone who may have used this in the past. First, do I specify the two contrasts to merge using the contrast flag twice? Ex: -contrast [name] [thresh] [tail] -contrast [name] [thresh] [tail] or do I specify both contrasts under a single tag? Additionally, this is a memory task and the encoding and retrieval runs were analyzed separately (same analysis type, but same coding in paradigm files and different sessions parent directories) so will it be possible to indicate to the program where the encoding contrast to be merged with the retrieval contrast is? Or will I have to rearrange my directories, recode my paradigm files, and make new contrasts? probably the latter huh? Topic 2, correlation analysis: As an alternative to a conjunction analysis, is it possible to use freesurfer to perform a voxel-by-voxel group level correlation analysis of encoding versus retrieval runs for a memory task perhaps obtaining a map of r-values or sigs or r values representing the correlation of the time courses from corresponding voxels from the two runs? what freesurfer tools would do this? Thanks in advance, Cameron > Oh, you want a "conjunction" I think. Corrlation means something else. > Try mergecontrasts-sess > > doug > > > > Cameron Ellis wrote: > >>Hi Doug, >>We would like to compare, voxel by voxel, the activity between two >>back-to-back runs, one encoding run and one retrieval run for a memory >>task. Ideally what we have in mind would be to view, on the inflated >>surface, a map of voxels that were above a certain threshold during both >>encoding and retrieval. Could we somehow make a whole brain functional >>mask from the encoding run an apply this to the retrieval run? >>Cameron >> >> >> >>>I'm not sure what you are trying to do. sound like you have two values >>>per voxel for each subject that you want to correlate, but you can't >>>really correlate two values. I think I'm missing something ... >>> >>>doug >>> >>>Cameron Ellis wrote: >>> >>> >>> >>>>Does anyone have an answer to this question? >>>> >>>>Hello, >>>> >>>>I am looking for a way to perform voxel-wise, within-subject >>>> correlations >>>>of two >>>>activation maps (in talairach space). The two existing maps reflect >>>>encoding >>>>and retrieval runs of a memory task. The idea would be to generate a >>>>correlation map across all subjects, to identify clusters where there >>>> was >>>>a >>>>positive or negative correlation between encoding and retrieval >>>>activation. >>>> >>>>I've seen this done with SPM but not Freesurfer. Any suggestions? >>>>(Perhaps >>>>this would involve glmfit?) >>>> >>>>Many thanks, >>>>Josh >>>>_______________________________________________ >>>>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 Center >>>greve(a)nmr.mgh.harvard.edu >>>Phone Number: 617-724-2358 >>>Fax: 617-726-7422 >>> >>>In order to help us help you, please follow the steps in: >>>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> >>> >>> >>> >>> >>> >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >

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Freesurfer June 2007