Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

nu_correct problem
by rega0026＠umn.edu 10 Jul '12

10 Jul '12

Hello, I am trying to run recon-all using freesurfer 5.1.0. This worked on most of my subjects, but for about 10 subjects, I got an error: nu_correct: Command not found I can see on the archive that several others have run into this problem, but I couldn't figure out from the archives what the solution is. I do have perl installed in usr/bin. Thanks very much, Katie -- Kathryn R. Cullen, M.D. Assistant Professor University of Minnesota Medical School Department of Psychiatry Division of Child and Adolescent Psychiatry (612) 273-9825

4 4

label transformation to MNI space
by Linda Douw 05 Jul '12

05 Jul '12

Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Linda Douw, PhD.

4 7

Extraction Longitudinal Stats
by Dídac Vidal 04 Jul '12

04 Jul '12

Hi everybody, I have a question about FS longitudinal post-processing. Currently I obtained some corrected results comparing a Control vs. an Experimental group (pre-post). What i would like to know is if there's a thinning in the control group or a increase in the thickness of the experimental group. I tought in create a label and extract the individual values of both timepoints and then do a t test in order to see if the mean differs to 0. How I can do that?; There is an easier way to do it? Thanks in advance -- Dídac Vidal Piñeiro Dept. Psychiatry and Clinical Psychobiology Faculty of Medicine University of barcelona

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/path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory
by Xiangzhen Kong 08 Jun '12

08 Jun '12

Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++ mv -f /xxx/dmri/dwi_orig_flip.mghdti.bvecs /xxxx/dmri/bvecs mv: cannot stat `/xxx/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory +++ I check the dir /xxx/dmri/ and there are only two files 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz' and a dir 'xfms'. Does trac-all extract bvals/bvecs automatically when start with DICOM data? My data is from a siemens scanner. Thanks! Xiangzhen 2012-02-03 Xiangzhen Kong

2 4

Re: [Freesurfer] Inter-hemispheric registration issue
by Douglas N Greve 04 Jun '12

04 Jun '12

Irene, this is a problem with the script. The work-around is to run xhemireg before running surfreg with the --xhemi option. doug On 05/16/2012 01:56 AM, Irene Altarelli wrote: > Dear Doug, > > here is what I get. > > First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the > attached log file. Here is the terminal output: > > setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ > cd /home/ialtarelli > /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym > --lh > > Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 > x86_64 GNU/Linux > #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200) > #CMD# mris_register -curv -annot > aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg > using smoothwm curvature for final alignment > zeroing medial wall in aparc.annot > $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ > $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ > reading surface > from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere... > reading colortable from annotation file... > colortable with 36 entries read > (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > reading template parameterization > from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... > ripping medial wall... > writing registered surface > to /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.007, std = 0.603 > curvature mean = 0.030, std = 0.806 > curvature mean = 0.024, std = 0.853 > curvature mean = 0.009, std = 0.826 > curvature mean = 0.011, std = 0.936 > curvature mean = 0.003, std = 0.836 > curvature mean = 0.005, std = 0.972 > curvature mean = 0.001, std = 0.837 > curvature mean = 0.001, std = 0.988 > curvature mean = -0.032, std = 0.312 > curvature mean = 0.032, std = 0.124 > curvature mean = 0.079, std = 0.315 > curvature mean = 0.031, std = 0.151 > curvature mean = 0.049, std = 0.489 > curvature mean = 0.031, std = 0.165 > curvature mean = 0.028, std = 0.631 > curvature mean = 0.031, std = 0.171 > curvature mean = 0.011, std = 0.749 > 159: 0 negative triangles > surfreg-Run-Time-Hours aa_tris lh 0 0,90 > mardi 15 mai 2012, 20:17:58 (UTC+0200) > surfreg done > > Then, I ran surfreg --s aa_tris --t fsaverage_sym --lh --xhemi and the > terminal output is just: > > ERROR: cannot > find /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/surf/lh.sphere > > without any log file, at least I can't find any modified file in the > subject's folder. > > > Hope this helps make things clearer. > Many thanks in advance! > Irene > > > Le mardi 15 mai 2012 à 15:19 -0400, Douglas N Greve a écrit : >> Can you send me the command line and terminal output? Did you run >> xhemireg first? Should not have had to ... >> >> On 05/15/2012 03:02 PM, Irene.Altarelli(a)ens.fr wrote: >>> Dear Doug, >>> >>> where would that log file be? As the /subject/xhemi fails to be created the log >>> normally appearing in there cannot be found.. Sorry if I misunderstood >>> something. >>> >>> Thanks, >>> Irene >>> >>> >>> Selon Douglas N Greve<greve(a)nmr.mgh.harvard.edu>: >>> >>>> Hi Irene, can you send the log file for the command that is failing? >>>> doug >>>> >>>> On 05/15/2012 01:28 PM, Irene Altarelli wrote: >>>>> Dear all, >>>>> >>>>> I'm trying to use the new script for the inter-hemisphere analysis, in >>>>> Fs version 5.0. I have downloaded the files as suggested >>>>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html) >>>>> >>>>> Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym >>>>> --lh), but I have problems then with the --xhemi option. Some files >>>>> appear to be missing, I get the following error messages: >>>>> >>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere >>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm >>>>> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere >>>>> ERROR: cannot find /path/subject/xhemi/label/lh.aparc.annot >>>>> >>>>> lh.fsaverage_sym.sphere.reg is created in $subject as it should (please >>>>> find the surfreg log below). >>>>> >>>>> Thank you in advance, >>>>> Irene >>>>> >>>>> >>>>> Log file for surfreg >>>>> samedi 12 mai 2012, 17:36:31 (UTC+0200) >>>>> >>>>> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ >>>>> cd /home/ialtarelli >>>>> /home/ialtarelli/freesurfer/bin/surfreg --s aa_copie --t fsaverage_sym >>>>> --lh >>>>> >>>>> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 >>>>> x86_64 GNU/Linux >>>>> #@# lh samedi 12 mai 2012, 17:36:31 (UTC+0200) >>>>> #CMD# mris_register -curv -annot >>>>> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere >>>> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif >>>> /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg >>>>> using smoothwm curvature for final alignment >>>>> zeroing medial wall in aparc.annot >>>>> $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ >>>>> $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ >>>>> reading surface >>>>> from /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere... >>>>> reading colortable from annotation file... >>>>> colortable with 36 entries read >>>>> (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>> reading template parameterization >>>>> from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... >>>>> ripping medial wall... >>>>> writing registered surface >>>>> to >>>> /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg... >>>>> curvature mean = 0.007, std = 0.603 >>>>> curvature mean = 0.030, std = 0.806 >>>>> curvature mean = 0.024, std = 0.853 >>>>> curvature mean = 0.009, std = 0.826 >>>>> curvature mean = 0.011, std = 0.936 >>>>> curvature mean = 0.003, std = 0.836 >>>>> curvature mean = 0.005, std = 0.972 >>>>> curvature mean = 0.001, std = 0.837 >>>>> curvature mean = 0.001, std = 0.988 >>>>> curvature mean = -0.032, std = 0.312 >>>>> curvature mean = 0.032, std = 0.124 >>>>> curvature mean = 0.079, std = 0.315 >>>>> curvature mean = 0.031, std = 0.151 >>>>> curvature mean = 0.049, std = 0.489 >>>>> curvature mean = 0.031, std = 0.165 >>>>> curvature mean = 0.028, std = 0.631 >>>>> curvature mean = 0.031, std = 0.171 >>>>> curvature mean = 0.011, std = 0.749 >>>>> 159: 0 negative triangles >>>>> surfreg-Run-Time-Hours aa_copie lh 0 0,84 >>>>> samedi 12 mai 2012, 18:26:49 (UTC+0200) >>>>> surfreg done >>>>> >>>>> >>>> -- >>>> 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 >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it is >>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>> contains patient information, please contact the Partners Compliance HelpLine >>>> at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>> error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>>> >>> -- 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

3 6

Using QDEC ROIs to extract text files of surface areas
by Cynthia Elisabeth Krafft 01 Jun '12

01 Jun '12

Hello, Sorry for the newbie question. I completed a group analysis in QDEC and drew a ROI, which I saved and mapped to the individual subjects. I'm interested in getting text output of the surface area for each individual within that ROI. Here is an example of the command that I ran for one person: mris_anatomical_stats -l lh.X.area.label -b -nsmooth 15 subject lh white The problem is that when I plot these values against the variable that I originally put in to the analysis (for which I got significant results in this ROI in QDEC), it doesn't look like there is anything there, so I guess I did something wrong or my interpretation is wrong. I'd appreciate any insight! Thanks, Cindy

3 2

(no subject)
by Kathryn I. Alpert 01 Jun '12

01 Jun '12

Dear Freesufer experts, I am wondering if it is possible to tell mri_vol2surf to ignore certain voxels in the src volume, for instance, by setting their intensity to -999. I'm trying to project only gray matter voxels from a PET scan onto the fsaverage surface, but when I use an only-GM PET image as the src, the zeroed-out WM/CSF voxels are occasionally projected onto the surface (with --interp nearest). Any suggestions? Thanks! Kate

3 2

tkregister question
by Shay Ohayon 01 Jun '12

01 Jun '12

Hi, Here's a question to Doug / anyone else who mastered the intricate way of volume transformations: I'm a bit puzzled. According to Free surfer's documentation (fscoordinates.pdf), the way two volumes are registered to each other using tkregister is always using the fixed transformation (tkvox2ras) (see page 6). However, when I do the following little experiment (using matlab's freesurfer API) A = '001.nii'; B = '002.nii'; X=MRIread(A); X.vox2ras0(1,4) = 40; MRIwrite(X,B); tkregister2 --targ 001.nii --mov 002.nii --regheader -reg R.reg The two volumes are not in alignment when they are loaded into tkregister. Now, what am I missing here? If both were loaded using the fixed transform, they should still be in alignment (i.e., vox2ras should be ignored for registration purposes). Thanks in advance, -- Shay Tsao lab Caltech

2 2

qdec: selecting multiple continuous variables
by Laura M. Tully 01 Jun '12

01 Jun '12

Hi, I am using freesurfer 5.1.0 and qdec 1.4. I'm interested in looking at between group differences in thickness in relation to two other continuous measures whilst controlling for ICV. However, qdec doesn't seem to let me select more that one continuous variable even though I only have group selected (discrete) and ICV (nuisance) as additional variables (i.e. a total of three selected) - it's my understanding that qdec allows up to 4 variables, is there a method to selecting multiple continuous variables that I am missing (e.g. hold down shift and select)? Thanks! Laura. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully(a)fas.harvard.edu -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura

2 1

transfer annot files from template to each subject
by Leon 01 Jun '12

01 Jun '12

Hi, FreeSurfer expert I am having difficulty finding the functions that transfer an annotation file I generated on a template to each subject. This template has been registered with several subjects using a surface-based registration method. Now what I want is to (1) transfer this annotation file from the template to each subject, through surface-based registration. and then (2) transfer the annotation file in each subject's surface to their T1 volume space. Could someone show me which functions I need to use? Do I have to convert the annotation files first to label files to do that? Many thanks in advance Leon

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Freesurfer May 2012