[Freesurfer] sequence]
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] sequence]
Hi Roberto, most of our stuff only works on the T1 (i.e. option 1). In general the T2/PD is impossible to register accurately to the T1, which is why we haven't used it in the past. We have some new sequences developed by Andre van der Kouwe that resolve this problem, but they aren't widely used yet. cheers, Bruce On Mon, 3 Dec 2007, Roberto Roiz Ssantiáñez wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_subject
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Retinotopy and MT+ localization analysis help
Hi Anisha, when you are debugging these things, it's best to go back as close to the raw data as possible (rather than looking at the final product on the flat map). Eg, try looking at the eccen and polar significance maps separately in the volume, then on the surface, then look at the phase maps in the volume and on the surface, etc. doug anisha narula wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] make_average_subject
If you want to do stats on your cohort, you should use mris_preproc and mri_glmft using the same subject list as you used to create the average subject (you can pass all three programs an fsgd file to make sure that you have the same in both). mri_glmfit will give you mean and std thickness as well as allow you to test hypotheses. doug Emily Trittschuh wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cluster thresholding
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=2.00 (2.00), thmax=-1.00 (-1), thsignid=0, minarea=25.00 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 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Error encountered while running selxavg3
Dear FreeSurfers, On my maiden voyage with selxavg3, I've encoutered an error and could use some help. After processing several subjects successfully, selxavg3 quit unexpectedly. Here is the exact message: Warning: matrix is singular to working precision In fast_selxavg3 at 208 ntptot = 666, nX = 31, DOF = 635 ??? Error using == svd Input to SVD must not contain NaN or Inf. Error in == cond at 40 s = svd(A); Error in == fast_selxavg3 at 235 XCond = cond(XtX); Can anyone help me track down the source of this error and/or suggest a fix? Also, in the course of reviewing the error I saw the following notice: INFO: Key -timeoffset unrecognized, line 7, skipping I have the timeoffset argument set to half a TR in my mkanalysis step because I included slicetime correction during preprocessing. Does selxavg3 not recognize this option? Thanks in advance for any help you can provide. Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cluster thresholding
Thanks for your help Pratap. I've actually been trying to follow the tutorial and was running simulations initially, but when I tried to re-trace my steps I ended omitted them because I forgot they were necessary for mri_surfcluster. Either way, the results are the same- I still get one whole surface cluster as output even after running simulations. In this case, I re- ran it copying your commands, except I used perm because I have low numbers and no covariates. I also ran 1000 permutations, to get a quick initial result for testing. My commands and output are below. I would appreciate further help on this, as I'm not sure where I'm going wrong! also, I noticed that after your mri_glmfit command, you added --i divided into 5000 each. Sorry, but I'm not sure what you meant by that. mri_glmfit --y qdec/MF_group_rh/y.mgh --fsgd qdec/MF_group_rh/ qdec.fsgd doss --surf fsaverage rh --fwhm 34.309616 --C qdec/ MF_group_rh/contrasts/Diff-1-2-Intercept.mat --sim perm 1000 2 stats/ newperm_rh/newperm_rh --glmdir stats/newperm_rh/ gdfReadHeader: reading qdec/MF_group_rh/qdec.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 group1 2 group2 INFO: gd2mtx_method is doss Reading source surface /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/rh.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/rh.white.avg.area.mgh simbase stats/newperm_rh/newperm_rh Number of vertices 163842 Number of faces327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566 reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/rh.white.avg.area.mgh INFO: fwhm2niters: Fixing group surface area Surface smoothing by fwhm=34.309616, niters=866.00 $Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ cwd /data/kang/work/struct/alex/freesurfer/subjects_cann cmdline mri_glmfit --y qdec/MF_group_rh/y.mgh --fsgd qdec/MF_group_rh/ qdec.fsgd doss --surf fsaverage rh --fwhm 34.309616 --C qdec/ MF_group_rh/contrasts/Diff-1-2-Intercept.mat --sim perm 1000 2 stats/ newperm_rh/newperm_rh --glmdir stats/newperm_rh/ sysname Linux hostname kang machine i686 user alex FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 34.309616 niters866.00 OneSampleGroupMean 0 y/data/kang/work/struct/alex/freesurfer/subjects_cann/qdec/ MF_group_rh/y.mgh logyflag 0 usedti 0 FSGD qdec/MF_group_rh/qdec.fsgd glmdir stats/newperm_rh/ DoFFx 0 Loading y from /data/kang/work/struct/alex/freesurfer/subjects_cann/ qdec/MF_group_rh/y.mgh Matrix condition is 1 search space = 82167.6 Smoothing input by fwhm 34.309616 Smoothing done, nsteps = 866, tsec = 1236.17 ... done DOF = 28 thresh = 2, threshadj = 2 Starting simulation sim over 1000 trials 1/1000 t=0 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Diff-1-2-Intercept 0 nc=3 maxcsize=1910.81 sigmax=-3.00831 Fmax=13.551 2/1000 t=0.0572833 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Diff-1-2-Intercept 1 nc=0 maxcsize=0 sigmax=1.36036 Fmax=4.46612 3/1000 t=0.0994333 ... and so on... then mri_surfcluster --src qdec/MF_group_lh/contrasts.sig.mgh --csd stats/ newperm_lh/newperm_lh-Diff-1-2-Intercept.csd --sum stats/newperm_lh/ newperm_lh --ocp stats/newperm_lh/newperm_lh.mgh thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = rh srcid = qdec/MF_group_lh/contrasts.sig.mgh paint srcsubjid = fsaverage srcsurf= white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr= -1 minarea= 0 xfmfile= talairach.xfm nth = -1 sumfile = stats/newperm_lh/newperm_lh 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/rh.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/rh.white.avg.area.mgh Done reading source surface Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max =
