Freesurfer December 2007

freesurfer@nmr.mgh.harvard.edu

45 participants
74 discussions

Re: [Freesurfer] Cluster thresholding
by Alexander Fornito 03 Dec '07

03 Dec '07

Hi all, I was hoping someone could help me with the problem below. I'm a little stuck on my analysis. Thanks, Alex > On 11/28/2007 07:43 PM, Alex Fornito wrote: >> Hi, >> I have run qdec for a simple contrast comparing thickness across the >> cortical surface between a patient and control group. Not much >> survives vertex-wise FDR correction, and I would like to try >> cluster-based thresholding. I would like to make sure I understand the >> inputs to the command. Am I correct on the following? >> >> --in = the signifcance values (i.e., contrast_name.sig.mgh file) >> --thmin = the vertexwise threshold for determining clusters, where 2 >> corresponds to p=.01 >> --minarea = the cluster extent threshold - Am I correct in assuming >> this should not be smaller than the smoothing kernel? >> >> When I run the command below, I get the following output. Only one >> (whole hemi) cluster is identified. I'm not sure if its a problem in >> my command line, or with my data. Also, I seem to have the --cwsig >> flag wrong, but can't figure out the error (appending .w or .label to >> the end of the output filename does not change the error). >> >> I greatly appreciate your help. >> >> >> mri_surfcluster --in qdec/MF_group_lh/contrasts.sig.mgh --subject >> fsaverage --hemi lh --surf white --annot aparc --sign abs --thmin 2 >> --minarea 25 --sum stats/qdec_run/cluster/summary.txt --o >> stats/qdec_run/cluster/cluster_output --cwsig >> stats/qdec_run/cluster/cwsig --olab >> stats/qdec_run/cluster/MF_group_lh_thk >> >> thsign = abs, id = 0 >> version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ >> hemi = lh >> srcid = qdec/MF_group_lh/contrasts.sig.mgh paint >> srcsubjid = fsaverage >> srcsurf = white >> srcframe = 0 >> thsign = abs >> thmin = 2 >> thmax = -1 >> fdr = -1 >> minarea = 25 >> xfmfile = talairach.xfm >> nth = -1 >> outid = stats/qdec_run/cluster/cluster_output paint >> sumfile = stats/run2/cluster/summary.txt >> subjectsdir = /data/kang/work/struct/alex/freesurfer/subjects_cann >> FixMNI = 1 >> ------------- XFM matrix (RAS2RAS) --------------- >> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/mri/transforms/talairach.xfm >> 1.000 0.000 0.000 0.000; >> 0.000 1.000 0.000 0.000; >> 0.000 0.000 1.000 0.000; >> 0.000 0.000 0.000 1.000; >> ---------------------------------------------------- >> Reading source surface >> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/surf/lh.white >> reading group avg surface area 822 cm^2 from file >> Reading in average area >> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/surf/lh.white.avg.area.mgh >> Done reading source surface >> Reading annotation >> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/label/lh.aparc.annot >> reading colortable from annotation file... >> colortable with 35 entries read (originally >> /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) >> Computing metric properties >> Loading source values >> number of voxels in search space = 163842 >> Done loading source values (nvtxs = 163842) >> overall max = 43.1907 at vertex 101931 >> overall min = 7.66111 at vertex 28089 >> surface nvertices 163842 >> surface area 65416.985991 >> surface area 65416.985976 >> NOT Adjusting threshold for 1-tailed test >> Searching for Clusters ... >> thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, >> minarea=25.000000 >> Found 1 clusters >> Max cluster size 103339.460938 >> INFO: fixing MNI talairach coordinates >> Saving thresholded output to stats/qdec_run/cluster/cluster_output >> avg = 35.029, stdev = 4.669, min = 7.661, max = 43.191 >> Saving cluster pval stats/qdec_run/cluster/cwsig >> unknown file type for file (stats/qdec_run/cluster/cwsig) >> LabelWrite: saving to stats/qdec_run/cluster/MF_group_lh_thk-0001.label >> >> >> >> Alex Fornito >> JN Peters Research Fellow >> Melbourne Neuropsychiatry Centre >> Department of Psychiatry >> The University of Melbourne >> >> Postal address: >> Melbourne Neuropsychiatry Centre >> National Neuroscience Facility >> Levels 2 & 3, 161 Barry St >> Carlton South Vic 3053 Australia >> >> Ph: +61 3 8344 1861 >> Fax: +61 3 9348 0469 >> >> fornitoa(a)unimelb.edu.au <mailto:fornitoa@unimelb.edu.au> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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make_average_subject
by Emily Trittschuh 03 Dec '07

03 Dec '07

Dear List, Awhile back Cameron Ellis wrote to the listserv to ask about stats files for make_average_subject results. He was looking for information on the # of vertices and I believe he found another way to obtain that info. I would like to revert to his orginal question of whether there is any way to generate an ?.aparc.stats file from the make_average_subject command. I have a group of older normal controls that I want to turn into an "average" subject. They (as a mean individual) will be used for comparison with individual patients with an unusual form of dementia. It seems that as I move the cursor over the ?.avg_thickness surface it IS showing local numbers for thickness, but I can't find any stats files that will provide me with the std dev for these measurements. In addition I would love to be able to compare the results of the cortical parcellations between subjects and the average subject. Thank you! Emily Emily Trittschuh, PhD Neuropsychology Post-doctoral Fellow Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11-579 Chicago, IL 60611 phone 312/503-1155 fax 312/908-8789

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Retinotopy and MT+ localization analysis help
by anisha narula 03 Dec '07

03 Dec '07

To whom it may concern, I am a beginner at FreeSurfer and using it in my senior biomedical design project at Boston University. I have performed retinotopy and MT+ localization before on a previous subject and obtained good results. However, I have carried out retinotopy and MT+ analysis on another subject using the same commands and have not obtained significant results. I have tried the analysis using motion corrected and motion uncorrected data, and have obtained bad results both times. I have attached the fieldsign image above obtained from the retinotopy analysis. Please let me know, if you would like to see the polar, eccentricity or MT+ images as well. I appreciate your time and concern Thank You, Anisha

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sequence]
by Roberto Roiz Ssantiáñez 03 Dec '07

03 Dec '07

Hello all, Im a new user of FreeSurfer. We would like to start processing a large number of the scans. We have acquired three different sequences using a 1.5T GE scanner (a three dimensional T1-weighted SPGR sequence, and two dimensional PD and T2 sequences). We have already processed those sequences using BRAINS2, and we have obtained a segmented image. I was wondering which sequence would fit best with FreeSurfer: 1) The T1-weighted SPGR sequence. 2) The T1-weighted SPGR sequence and the PD sequence together. 3) The segmented image obtained using BRAINS2. Thanks a lot Roberto Roiz ______________________________________________ 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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Freesurfer December 2007