Freesurfer

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30084 discussions

Gaussian random field correction
by Jürgen Hänggi 06 Jul '09

06 Jul '09

Dear FS experts Is the GRF correction for multiple comparisons implemented in FS yet and is there any documentation how to use it? Thanks in advance Best regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division 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[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 1

recon-all freezing
by Dana W. Moore 06 Jul '09

06 Jul '09

Hi all, I have been trying to process an image, and the reconstruction has been consistently freezing at the same spot. This brain failed the tailarach transform, but I checked it and it looked fine, so I used the -notal-check flag. I have had this happen with several other brains, and there was no problem using this flag until now. I have tried it on 2 different computers where we have FreeSurfer, and it still freezes at the exact same place. I left it overnight to be sure it was really frozen, and the next morning the reconstruction script had not progressed. There is no error message. The place where it freezes is mri_ca_normalize, and I have pasted the script below: #@# CA Normalize Thu Jul 2 18:31:14 EDT 2009 /home/dwm2003/NPH/FS/NPH3/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (56, 38, 29) --> (205, 184, 175) using (106, 87, 102) as brain centroid... mean wm in atlas = 107, using box (88,69,84) --> (124, 104,119) to find MRI wm before smoothing, mri peak at 88 after smoothing, mri peak at 87, scaling input intensities by 1.230 scaling channel 0 by 1.22989 using 244171 sample points... INFO: compute sample coordinates transform 0.926 -0.053 0.111 2.200; 0.005 0.987 0.482 -32.821; -0.126 -0.444 0.940 78.347; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (124, 43, 29) --> (200, 162, 179) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 110.0 115 of 354 (32.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (58, 45, 28) --> (131, 156, 177) This is always where the script stops when the process seems to freeze. (I have tried 3 times with the same result). Any ideas? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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Citing FreeSurfer in Papers - GLM - Thickness Analysis
by Pedro Paulo de Magalhães Oliveira Junior 02 Jul '09

02 Jul '09

I'm co-writing a paper using FreeSurfer and reading the Wiki page regarding how to cite FreeSurfer: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation <http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation>When we cite the mri_glmfit we usually use as reference: Fischl B, Sereno MI, Tootell RB, Dale AM. High-resolution intersubject averaging and a coordinate system for the cortical surface. *Hum Brain Mapp *1999; *8*: 272-284. However we use mri_glmfit-sim for multiple comparisson correction. Is this paper the citation for mri_glmfit-sim ? ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business

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monte-carlo simulation question
by Prapti Gautam 02 Jul '09

02 Jul '09

Dear Freesurfers, I ran a monte carlo simulation for thickness analyses using mri_glmfit and found new files in the contrast subdirectory. I was able to figure out what the first two represent, but was wondering if any one could clarify what information the rest of the files show: mc-z.negative.sig.cluster.summary : cluster summaries mc-z.negative.sig.ocn.annot : annotation of clusters mc-z.negative.sig.cluster.mgh : mc-z.negative.sig.ocn.mgh : mc-z.negative.sig.voxel.mgh : Thanks very much for your help, Prapti

2 1

Brain segmentation stats
by Jared Price 01 Jul '09

01 Jul '09

Gurus, Looking over some stats recently I noticed that if you add up all of the freesurfer stats for ventricles, namely the left and right lateral ventricles plus 3rd, 4th, and 5th ventricles and subtract that from the "Number of Brain Segmentation Voxels" stat, you do not get the value of the "Brain Segmentation Volume Without Ventricles" stat. Anyone know why?

2 1

Freesurfer FSL Dimensions
by Natalia Sanchez 01 Jul '09

01 Jul '09

Hi: I am using Freesurfer and FSL together. My image dimensions initially are 256x256x128 in nii.gz format. I convert these images to .mgz using mri_convert and do cortical and subcoritcal segmentation in FreeSurfer. The outputs of the segmentation are the converted back into .nii.gz so I can use them in FSL, however, the dimensions of the Freesurfer outputs don't match with the FSL files. The freesurfer outputs are 256x256x256. Is there a way I can downsample this outputs to use them in FSL? Thanks!

2 1

mri_glmfit error
by Susie Heo 01 Jul '09

01 Jul '09

Hello, I am trying to run a cortical thickness analysis to look for an interaction between two continuous variables using mri_glmfit. I created an fsgd file including only the two original CVs to investigate main effects and obtained the output. When I added the interaction term (product of the two CVs) as a third continuous variable in my fsgd file and tried to run a dods analysis, I received the message: "ERROR: matrix is ill-conditioned or badly scaled." I don't understand how this could be the case. Is there a simple way to check whether my design matrix is ill-conditioned? Susie

2 1

mkbrainmask not finding fslmaths
by dahlia＠nmr.mgh.harvard.edu 01 Jul '09

01 Jul '09

Hi, I ran the following preproc-sess command and mkbrainmask-sess failed, with an error message of not finding fsmaths. I don't know where to be looking for this file and what previous command should have generated it. Can anyone help me out? Thanks! Dahlia. I ran: preproc-sess -sf sessid_subj31.txt -df sesspar -fwhm 5 The error message was: ERROR: cannot find either fslmaths for avwmaths ERROR: mkbrainmask failed ERROR: mkbrainmask-sess failed mkbrainmask-sess.log says: mkbrainmask-sess $Id: mkbrainmask-sess,v 1.12.2.1 2008/10/02 21:56:15 greve Exp $ Linux mbc.stanford.edu 2.6.22.9-61.fc6 #1 SMP Thu Sep 27 18:07:59 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux Tue Jun 30 11:01:46 PDT 2009 /home/dahlia.sharon/functionals/fba_study_mtloc -maskstem brain -fsd bold -s mtloc_19may07 -d /home/dahlia.sharon/functionals/subj31 -update This is the command preproc-sess invoked: mkbrainmask -i 025/f.bhdr -o masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0 The data is not on the network so I can't give paths.

2 2

Multiple Comparison - Clusterwise Correction
by Devdutta W 01 Jul '09

01 Jul '09

Hi Freesurfers, More questions about this analysis. 1) Referring to the documentation, we used the following command: tksurfer fsaverage lh inflated -annot mc-z.abs.2.sig.ocn.annot -fthresh 2 -curv -gray The documentation says we should see an image as shown in Figure 1 (attached). But what we see is Figure 2 (also attached). Can somebody explain this? 2) When running the simulation does it matter what threshold we use? For example, can we use a threshold of 2 or 3 (instead of 4 as shown in documentation) when running mri_glmfit-sim? And do we have to use the same threshold while displaying the clusters after? Thanks for any help. Devdutta

4 14

standardize in asegstata2table
by Anita di Iasio 01 Jul '09

01 Jul '09

Hi all, I have a question. In the table created from asegstats2table, are the volumes standardized to Talairach space? or are they in their orig space? thank in advanced, anita

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