Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Problem creating longitudinal template file
by Corinna Bauer 15 May '12

15 May '12

Hello all, I am trying to create a template for longitudinal processing and am running into some problems generating the file. I have many subjects so I am running a batch script. I am using version 5.1.0 Any suggestions? Thanks! Corinna Here is my script: #!/bin/tcsh setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv SUBJECTS_DIR /Applications/freesurfer/subjects/corinna/ADNI/template set subjects=`cat $1` foreach subject ($subjects) echo "-------------------- Processing $subject -------------------------" set subj_dir=/Applications/freesurfer/subjects/corinna/ADNI/ set template=/Applications/freesurfer/subjects/corinna/ADNI/template/${subject}_template/mri set tp_BLmos=/Applications/freesurfer/subjects/corinna/ADNI/BL/${subject}/mri/norm.mgz set tp_12mos=/Applications/freesurfer/subjects/corinna/ADNI/12mos/${subject}/mri/norm.mgz set tp_24mos=/Applications/freesurfer/subjects/corinna/ADNI/24mos/${subject}/mri/norm.mgz set tp_36mos=/Applications/freesurfer/subjects/corinna/ADNI/36mos/${subject}/mri/norm.mgz #set nu_mgz=${subj_dir}/mri/nu.mgz recon-all -base ${subject}_template -tp ${tp_BLmos} -tp ${tp_12mos} -tp ${tp_24mos} -tp ${tp_36mos} -all end Here is my output: -------------------- Processing 137_S_0631 ------------------------- Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/corinna/ADNI/template Actual FREESURFER_HOME /Applications/freesurfer Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2: Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# Longitudinal Base Subject Creation Mon May 14 18:21:23 EDT 2012 /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template \n mri_robust_template --mov /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz --lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta --template /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz --average 1 --sat 4.685 \n $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. Total: 4 input volumes --lta: Will output LTA transforms --template: Using /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz as template output volume. --average: Using method 1 for template computation. --sat: Using saturation 4.685 in M-estimator! reading source '/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz'... mghRead(/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz, -1): could not open file MultiRegistration::loadMovables: could not open input volume /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz. Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2: Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64 recon-all -s 137_S_0631_template exited with ERRORS at Mon May 14 18:21:23 EDT 2012 For more details, see the log file /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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recon-all exiting with errors
by Richter, Julia 15 May '12

15 May '12

Dear FreeSurfer experts, I am trying to recon-all T1 images with the command recon-all -s <subjectname> -i /path/to/subject/directory/subject.nii.gz. This command used to work with several images, but one of my images is always exiting with errrors, in my opinion without a reason. Any suggestions what is going on? I am attaching the recon-all.log of my data. Thanks for your help, Julia

2 1

Need some materials
by bowang21＠mail.ustc.edu.cn 15 May '12

15 May '12

Dear Freesurfer Experts, I am a senior, and I am going to finish my graduation thesis which is about the use of freesurfer.So I need some written materials,such as the development history of Freesurfer, the achievement of Freesurfer and so on. But I don't know. Can you help me? Or give me some wed pages. Thanks in advance. Yours Bobo

2 1

"cannot allocate memory" issue
by Borzello, Mia 14 May '12

14 May '12

Hi all, I was wondering if you could help me figure out why the recon isn't running to completion. I've attached the log file (recon-all.log), but it's unclear to me what I should do to fix this problem. I tried to compute the lh.pial, but I guess it was never made in the recon. Thanks so much, Mia

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optseq2 event duration definition
by Andrew Valdespino 14 May '12

14 May '12

(1) Version: optseq2.c,v 2.21.2.1 (2) Computer operating system: Mac OS X Version 10.7.3 (3) Command line: Not relavant here (4) Description of the problem: A trial in my experiment involves a countdown (duration 2 seconds) followed by the event of interest (0.5 seconds) followed by a blank screen (3.5 seconds). I am having trouble with the definition of 'event duration'. That is, for the argument --ev x *y* z, what do I specify for *y *(event duration)? the entire trial is 7 seconds in length, but the duration of the event of interest is only 0.5 seconds (embedded between a countdown, and a blank screen). As a second question, is psdmin always set at '0'? Would '0' be appropriate for the trial structure described above? (5) Log and/or summary files: Not relavant here ________

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Re: [Freesurfer] optseq
by Douglas N Greve 14 May '12

14 May '12

Hi Hanah, I found another bug with the way that tNullMin was being implemented which causes this problem. You can get the new version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2.linux doug On 05/14/2012 08:47 AM, Hanah Chapman wrote: > Dear Doug, > > Thank you for your response to my question about optseq and > tnullmin/max on the freesurfer listserv. The new file you sent did fix > the problem where some null trials exceeded the tnullmax, but I'm > still having difficulty calculating the correct number of timepoints. > I always get one very long (~60s) null event at the end. My starting > approach was to compute the average length of the null trial within > the range of tnullmin-tnullmax, and then allow that much time between > each trial. I also tried to reduce the number of timepoints in steps, > but I still get the problem of the long null at the end right up until > the point that optseq returns an error (presumably because there are > not enough timepoints). If you can offer any insight, that would be > much appreciated. The starting code in which I used an average of 7s > between each trial is this: > > > ./optseq2.linux --ntp 360 --tr 2 --tnullmin 4 --tnullmax 10 --psdwin 0 > 20 --nkeep 6 --o ./attention/360tp --nsearch 1000 \ > --ev DD 2 5 \ > --ev DF 2 5 \ > --ev DP 2 5 \ > --ev DN 2 5 \ > --ev FF 2 5 \ > --ev FD 2 5 \ > --ev FN 2 5 \ > --ev FP 2 5 \ > --ev PP 2 5 \ > --ev PD 2 5 \ > --ev PN 2 5 \ > --ev PF 2 5 \ > --ev NN 2 5 \ > --ev ND 2 5 \ > --ev NF 2 5 \ > --ev NP 2 5 > > Thanks for your help, > > Hanah > > -- > > Hanah Chapman > Postdoctoral Fellow > Department of Psychology > The Ohio State University -- 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

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Edit Aseg with Surfaces
by Matt Glasser 14 May '12

14 May '12

Is there a way to adjust the grey and white matter of the aseg automatically based on the surfaces? Thanks, Matt.

2 1

mri_glmfit-sim error
by Juke Cha 14 May '12

14 May '12

Hi all, I've got an error while running mri_glmfit-sim. I ran this for several measures, and only for 'volume' and 'area' the function complained about missing CSD files stating "ERROR: cannot find any csd files" I don't know if this is a known issue. I saw several threads posted regarding this issue, but did not see a solution. Any suggestion? Best, Juke

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Re: [Freesurfer] How to convert a surface to volume space after using mris_preproc?
by Douglas N Greve 14 May '12

14 May '12

I don't know what that means. It is not an FS issue, it is something wrong on your system. doug On 05/14/2012 06:17 AM, Long wrote: > Hi Douglas, > > I used the command: > > tkmedit fslt1mnifs orig.mgz ./lh.zmap.mgh > > but it said: Resource temporarily unavailable. > > Best, > Xiangyu > > On Tue, Apr 24, 2012 at 5:01 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > How does it look in tkmedit? > > > On 04/23/2012 12:20 PM, Long wrote: > > Hi Douglas, > > I tried to do spatial normalization for volume data, all steps > are following: > > 1) bbregister --mov fsubj01_rest_res_co_001.hdr --bold --s > subj01 --init-fsl --reg bb_register.dat > > I checked the result by tkregister2, it looked good. > > 2) mris_preproc --target fsaverage --hemi lh --iv > fsubj01_001.hdr bb_register.dat --projfrac 0.5 --out lh.zmap.mgh > > 3) mri_surf2vol --surfval lh.zmap.mgh --hemi lh --identity > fsaverage --outvol subj01_001.nii.gz --projfrac 0.5 > --fillribbon --template wfrest_res_co_001.hdr > > However, the output file subj01_001.nii.gz showed wrong > orientation when viewing in MRIcron, the image looked rotated. > Could you please help with it? > > Best, > Xiangyu > > On Mon, Apr 23, 2012 at 4:31 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Hi Xiangyu, just add --identity fsaverage to the surf2vol > command line > doug > > > On 04/19/2012 05:57 PM, Long wrote: > > Hi all, > > > > I had a question when convert a surface to volume space. > > > > First, I converted a volume nifti data to fsaverage: > > > > mris_preproc --target fsaverage --hemi lh --iv data.nii > > bb_register.dat --out data.lh.mgh > > > > Then, I want to convert the data.lh.mgh to volume space, I tried > > mri_surf2vol, however, it needs register.dat. As I > understood, the > > data.lh.mgh was already registered to fsaverage surface, so how > can I > > get the required register.dat file? Thank you for your > attention. > > > > Best, > > Xiangyu > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- 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

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tfl single echo siemens ve‭rio te adjustment
by Jörg Pfannmöller 14 May '12

14 May '12

Dear freesurfers, currently the freesurfer single tfl protocol for the segmentation of the cortex surface was implemented at our scanner. Siemens Verio 3T MRT NumarisVer syngo MR B17 Gradientensystem (Tim 102x8) VQ-Engine Unfortunately the echo-time (te) could not be set to the recomended value of 3.31ms. The te is defined by the system and can not be changed. Is this critical for the segmentation quality? Sincerely yours A MRT-Physician

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Freesurfer May 2012