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Re: [Freesurfer] FSGD Contrast Setup Question
by Douglas N Greve 15 Sep '11

15 Sep '11

Hi Josh, there is not a way that I know of to do the paired analysis if some are missing a scan. A "real" statistician might know of a way theoretically, and I might be able to implement that theory, but I don't know myself. So does that mean you want to do an unpaired test? doug Roffman, Joshua L.,M.D. wrote: > Hi Doug, > Thanks for weighing in. For this study, while most subjects have 2 sets of good > scan data (pre and post treatment), a number have only one set (pre or post). > We're hoping to use all of the data given that it's overall a pretty small > study. Is it possible to run the paired analysis if we are missing pre or post > data for some subjects? > Best, > Josh > > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Thu 9/15/2011 4:54 PM > To: Adam Nitenson > Cc: freesurfer(a)nmr.mgh.harvard.edu; Roffman, Joshua L.,M.D. > Subject: Re: [Freesurfer] FSGD Contrast Setup Question > > Hi Adam, you have a "repeated measures" design. In your case, this is > best handled using a paired analysis. You can search for "paired" on the > wiki to get instructions. The easiest way to do this is to run > mris_preproc with the --paired-diff option, then follow the instructions > for the "standard" one or two group analysis (search for "fsgd"). > > doug > > Adam Nitenson wrote: > >> Hi Freesurfers, >> >> I am trying to set up both a 2 Group 1 Covariate and a 4 Group 1 >> Covariate analysis but just want to make sure I'm using the correct >> contrast option. >> >> For the first analyis, the two groups are Drug Pre and Drug Post, >> with folate-serum level as a covaraite. We want to keep the covariate >> under consideration in our analyses, but we really want to look at >> the difference between the Drug Pre and Drug Post activation (so >> folate-serum level is more of a nuisance variable). It seems that the >> first option under the 2G1V Page "Null Hypothesis: is there a >> difference between the group intercepts? Is there a difference >> between groups regressing out the effect of age? 1 -1 0 0" >> reflects this idea best. >> >> For the second analysis, the 4 Groups are Drug Pre, Drug Post, >> Placebo Pre, and Placebo Post, with the same folate-serum level >> covariate. We are intersted in the double subtraction of (Drug Post >> - Drug Pre) MINUS (Placebo Post - Placebo Pre), but again wish to >> covary by folate level. For this it seems like contast 7 on the 4G1V >> page "is there an interaction between gender and handedness >> regressing out the effects of age? 0.5 -0.5 -0.5 0.5 0 0 0 >> 0" is best. >> >> Is this the best way to go about analyzing these two questions? >> >> Thanks, >> >> Adam Nitenson, B.S. >> Brain Genomics Lab >> Massachusetts General Hospital >> nitenson(a)nmr.mgh.harvard.edu >> Phone: 617-643-3215 >> _______________________________________________ >> 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 1

GLM or Qdec ?
by Antonella Kis 15 Sep '11

15 Sep '11

Dear FS experts, I finished running the GLM and I wonder what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my patients versus control group. 1). Why when I overlay the sig.mgh in tksurfer lh inflated, I get more clusters than the number of clusters obtained from mri_glmfit-sim? 2). What sig.mgh represents? 3) What's the real significance of a cluster (how a cluster is formed)? 4). Why my thickness value in clusters (eg cluster no. 1 which coresponds to the posteriorcingulate) for subject no.1 is different that the thickness value obtained for the same region in the lh.aparc.stats while running recon-all? 5). After running the GLM should I use visualizing and plotting method to further analyse my data and load FSGD file lh.gender_age.glmdir/y.fsgd? 6). Should my ROI's be defined or be the same with my clusters? 7). What is the difference between GLM and Qdec? What method is the best to analyse the relation between age and cortical thickness for my patients versus control group? 8). Why when analysing with Qdec I get more clusters? Are this defining or representing the sig.mgh as in GLM? 9). When using Qdec were I can find as an output of results the number of clusters and the cortical thickness value? Thank you and have a great day! Antonella

3 13

using mri_label2label with full path
by Chris 15 Sep '11

15 Sep '11

I have a tricky situation where we can't use symbolic links ( cifs/smb mounts ) and it doesn't make sense to copy the fsaverage to the SUBJECTS_DIR. The subjects_dir is actually a separate directory for every subject when trying to run things through the connectome toolkit. I've edited my own version of recon-all in attempts of passing full paths to some of the tools if necessary. I'm getting caught in the mri_label2label step, since its using "--srcsubject" and "--srclabel" Passing a full path to "--srcsubject" doesn't work as expected, since its assuming the path of --srcsubject exists inside my SUBJECTS_DIR. If i only pass the default "fsaverage", then that also doesn't work because it doesn't exist inside my SUBJECTS_DIR either. Any suggestions? -Chris [petty@node61 free]$ mri_label2label --srcsubject /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage --srclabel /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/label/lh.BA1.label --trgsubject test20090520_36099 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/label/lh.BA1.label srcsubject = /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage trgsubject = test20090520_36099 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free/ FREESURFER_HOME /usr/local/packages/freesurfer_v5.1.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free///usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/surf/lh.sphere.reg MRISread(/mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_tes…: could not open file No such file or directory ERROR: could not read /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free///usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/surf/lh.sphere.reg

2 1

FSGD Contrast Setup Question
by Adam Nitenson 15 Sep '11

15 Sep '11

Hi Freesurfers, I am trying to set up both a 2 Group 1 Covariate and a 4 Group 1 Covariate analysis but just want to make sure I'm using the correct contrast option. For the first analyis, the two groups are Drug Pre and Drug Post, with folate-serum level as a covaraite. We want to keep the covariate under consideration in our analyses, but we really want to look at the difference between the Drug Pre and Drug Post activation (so folate-serum level is more of a nuisance variable). It seems that the first option under the 2G1V Page "Null Hypothesis: is there a difference between the group intercepts? Is there a difference between groups regressing out the effect of age? 1 -1 0 0" reflects this idea best. For the second analysis, the 4 Groups are Drug Pre, Drug Post, Placebo Pre, and Placebo Post, with the same folate-serum level covariate. We are intersted in the double subtraction of (Drug Post - Drug Pre) MINUS (Placebo Post - Placebo Pre), but again wish to covary by folate level. For this it seems like contast 7 on the 4G1V page "is there an interaction between gender and handedness regressing out the effects of age? 0.5 -0.5 -0.5 0.5 0 0 0 0" is best. Is this the best way to go about analyzing these two questions? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

2 1

mri_mcsim and mri_glmfit-sim
by MCLAREN, Donald 14 Sep '11

14 Sep '11

I am trying to figure out how to cluster some data on the cortical surface; however, I've run into a few issues: (1) I can't seem to find a description or examples for running mri_mcsim and mri_glmfit-sim won't work because I'm not using FSFAST to create my statistical maps. (2) A previous email suggested that there are stored values that I could lookup, but I can't seem to locate the files anywhere. (3) With respect to the fwhm values used in the simulations, it was suggested that this be matched to the fwhm.dat file output from mri_glmfit; however, since I didn't use mri_glmfit, I don't have fwhm.data file. Should I just use the smoothing used on the surfaces? Any thoughts would be appreciated. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

2 1

Converting a cluster to a ROI without manually drawing
by Nasim Maleki 14 Sep '11

14 Sep '11

Hi all, In qdec, is there a way to convert a cluster to an ROI without manually drawing the ROI? I'm talking about selecting clusters on the mc-z maps. Thanks, Nasim

2 2

statical question recon-all -qcache -s (subject) ?
by Knut J Bjuland 14 Sep '11

14 Sep '11

Hi Can I use a different version of Freesurfer to run recon-all -qcache -s (subject) than the version used for recon-all -all -s (subject)? Knut J

4 3

.img extension read as analyze even though hdr says nifti1
by Satrajit Ghosh 14 Sep '11

14 Sep '11

hi all, when a .img extension file is passed to freesurfer routines, it is read in as analyze even if the header says it's a nifti image. we have observed that this causes a left-right flip in some cases. since a .img cannot exist without a header to be meaningful, shouldn't the appropriate type be detected from the header? also it would be good to know if this behavior is consistent across all of freesurfer or restricted to certain binaries. see below for mri_info output cheers, satra $ mri_info con_0001.img Volume information for con_0001.img type: analyze4d dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 dof: 0 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.0000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.0000 0.0000 0.0000 78.0000 0.0000 2.0000 0.0000 -112.0000 0.0000 0.0000 2.0000 -50.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -8 ras to voxel transform: -0.5000 0.0000 0.0000 39.0000 -0.0000 0.5000 -0.0000 56.0000 -0.0000 -0.0000 0.5000 25.0000 0.0000 0.0000 0.0000 1.0000 $ mri_info con_0001.hdr Volume information for con_0001.hdr type: nifti1 dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 dof: 0 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.0000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.0000 0.0000 0.0000 78.0000 0.0000 2.0000 0.0000 -112.0000 0.0000 0.0000 2.0000 -50.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -8 ras to voxel transform: -0.5000 0.0000 0.0000 39.0000 -0.0000 0.5000 -0.0000 56.0000 -0.0000 -0.0000 0.5000 25.0000 0.0000 0.0000 0.0000 1.0000

2 1

flipped orientation in tksurfer and tkmedit
by Ilana Hairston 14 Sep '11

14 Sep '11

Hi there, We recently had a problem that tksurfer and tkmedit were flipped relative to each other. Basically, when saving a point in the left hemisphere in tksurfer it it loaded in the right hemisphere in tkmedit. Any ideas how this could have happened? Thanks ilana -- ****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

2 1

mean and stdev group-wise
by Tetiana Dadakova 14 Sep '11

14 Sep '11

Dear list, I would like to calculate mean and stdev of thickness group-wise. Could you please give me a hint how to do it? Thank you, Tanja.

2 1

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