Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

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

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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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tkmedit-sess question
by Avram Holmes 05 Jun '07

05 Jun '07

FreeSurfer Folks, I am attempting to look at some data with tkmedit-sess tkmedit-sess -analysis LowTraumaSPMHRF -contrast all_v_fix -d . -s FPPREW09 -map sig -fsd bold but I am getting the following error. corRead(): can't open file /exp/REfMRI/fMRI_FPPREW/structural//FPPREW09/mri/orig/COR-.info Error: Loading volume orig Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. I can look at the data with tkmedit (without the sess) loading all the files manually. I have tried the tkmedit-sess several different ways but I always get an error. Does anyone have an idea about how I get this to work? Thanks, Avram ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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how to import private color scales
by Istvan Akos Morocz 04 Jun '07

04 Jun '07

dear freesurfers, how do i import my own 'private' colorscales, i.e., colormaps for the overlay data ? something richer in colors than 'heat' ? what's the format and size for such a file? thanks, bye, pisti ----- pisti(a)bwh.harvard.edu

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