Freesurfer June 2010

freesurfer@nmr.mgh.harvard.edu

97 participants
138 discussions

Alignment problem
by Dankner, Nathan (NIH/NIMH) [F] 04 Jun '10

04 Jun '10

Hello all, I just ran a scan through autorecons 1 and 2, and the surface came out rotated approximately 45 degrees upwards from the front. Will this be a problem when I go to analyze, and if so, how do I go about correcting it? Thanks, Nathan

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subsampling Error with mri_convert of 4D .nii ?
by caspari＠clipper.ens.fr 04 Jun '10

04 Jun '10

HI! I need to subsample my original 4D .nii files (the f.nii or the fmc.nii after motion correction) from 2.5 2.5 2.75 to 2 2 2 mm, in each orignial 4D nii are 200 volumes: After subsampling with mri_convert -vs 2 2 2 001/fmc.nii 001/fmc.nii -oi -ii the output info tells me that the inputstructure changed from nframe 200 to nframe 1 (in outputstructure) as a consequence my subsequent analysis of the estimation of the statistics (-selxavg3-sess, not important I guess) cannot be performed. if I do the same for the f.nii files, the same happens, and -preproc-sess enters with an ERROR ('cannot perform mc') How can I keep my 200 frames in the 4D nii and subsample my voxels at the same time, to then continue my statistics? I would be extremely greatful I someone can help! Natalie xxx

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Re: [Freesurfer] cannon open .mgh file using MRIread
by corinna bauer 04 Jun '10

04 Jun '10

When I run mri_info I get: Volume information for /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac.35.mgh type: MGH dimensions: 23334 x 1 x 5 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 23334.000 dof: 0 xstart: -11667.0, xend: 11667.0 ystart: -0.5, yend: 0.5 zstart: -2.5, zend: 2.5 TR: 3000.00 msec, TE: 3.61 msec, TI: 1000.00 msec, flip angle: 8.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 5.5017 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 11.5254 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 11672.5020 0.0000 0.0000 1.0000 9.0254 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 11672.5020 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 -9.0254 0.0000 0.0000 0.0000 1.0000 On Fri, Jun 4, 2010 at 9:58 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > if you run mri_info on the .mgh file does it return reasonable looking > values? > > On Fri, 4 Jun 2010, corinna bauer wrote: > > Hi Bruce, >> I am having trouble getting my .mgh files to open in MRIread. I get the >> following error message. >> >> ERROR: could not open /home/freesurfer4.4.0/ >> subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac35.mgh for reading >> ERROR: loading >> >> /home/freesurfer4.4.0/subjects/corinna/ADNI/003_S_1057/mri/lh.white.projfrac35.mgh >> as MGH >> ??? Attempt to reference field of non-structure array. >> >> Error in ==> gwRatio at 24 >> gwratio.vol = gray.vol / white.vol; >> >> >> here's my .m file >> >> function gwRatio >> >> rootdir = '/home/freesurfer4.4.0/subjects/corinna/ADNI'; >> paths=dir([rootdir,'/*']); >> >> numel(paths) >> num = numel(paths); >> >> for ii = 1:num >> if(paths(ii).isdir && ~strcmp(paths(ii).name,'.') && >> ~strcmp(paths(ii).name,'..')) >> >> graypath= >> fullfile(rootdir,paths(ii).name,'mri/lh.white.projfrac35.mgh'); >> whitepath = >> fullfile(rootdir,paths(ii).name,'mri/lh.white.projdist.neg1.mgh'); >> outpath = fullfile(rootdir,paths(ii).name,'mri/lh.gwratio.mgh'); >> >> fprintf('----- Processing %i of %i -----\n', ii, num); >> fprintf('gray: %s\n', graypath); >> fprintf('white: %s\n', whitepath); >> fprintf('out: %s\n', outpath); >> >> gray = MRIread(graypath); >> white = MRIread(whitepath); >> gwratio = gray; >> gwratio.vol = gray.vol / white.vol; >> MRIwrite(gwratio, outpath); >> end >> end >> >> corinna >> >> > > 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. > >

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Using Freesurfer's label files to create one ROI
by Christophe Destrieux 04 Jun '10

04 Jun '10

Hi Stephan You could use mris_translate_annotation <subject> <hemi> <in annot> <translation file> <out annot> with : *<subject>* : the subject you want to work on *<hemi> *: the hemi you want to work on *<in annot> *: your initial annotation file (ie the one containing Medial OFC, Lateral OFC, anterior part of the Cingulate) *<translation file>* : a text file you have to create, that will list the labels( one per line) you want to group, and the new label you want to create. In fact you can't use the labels names but you have to use their RGB codes; each line will provide the input and output RGB values for instance the following file 221 220 60 223 220 60 221 220 160 223 220 60 221 220 100 223 220 60 will group 3 labels (with RGB codes 221 220 60, 221 220 160, and 221 220 100) in a single label (223 220 60) you can get the RGB value by clicking view->information->annotation on tksurfer interface after loading the surface and the annotation file. Be carefull not to use a RGB code previously used in your input annotation. You can get the RGB value of any label by clicking view->information->annotation on tksurfer interface after loading the surface and the annotation file. A field named annotation will be created on the interface with the RGV under brackets *<out annot>* : the output annotation (the one you want to create, with labels grouped together) cheers -- Christophe Destrieux, Directeur du Département Communication et Multimedia http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=120065115… Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 37032 Tours - France tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07

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recon-all -all -long error
by Gregory Dierksen 04 Jun '10

04 Jun '10

While running the following command: recon-all -all -long 2615_12202006 2615_12202006 -i .../dicom_raw/000001.dcm I'm getting this error durring the Cortical Ribbon mask: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 2615_12202006.long.2615_12202006 SUBJECTS_DIR is /autofs/space/eesmith_001/users/dierksen/Petichial WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. WARNING: the source volume info is not consistent between WARNING: the info contained in the surface data and that of the transform. Segmentation fault This happened for three subjects. And I should mention that these subjects have significant hemorrhages that caused failed surface recons in the cross sectional processing stream. This was fixed by "patching" in the hemorrhage in the wm.mgz, effectively forcing the wm surface to wrap around the hemorrhage area. So, what's going on? What can I do to fix this? Thanks, Greg --

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Using Freesurfer's label files to create one ROI
by Stefan Du Plessis 04 Jun '10

04 Jun '10

Hello everyone I looked through the Wiki and mailing list archives and could not find a page that directly addresses this issue. I want to create a ROI that consists of the Medial OFC, Lateral OFC, anterior part of the Cingulate etc. using freesurfer's labels. I dont want to hand draw my own ROI just yet. Then I want to run a regression analysis across this with mri_glmfit. What is the simplest way of doing this on the command-line? It seems simple on QDEC, but I could not find it in the mri_glmfit command line documentation. (It just says --label **** add your label here...) PS When I upload a file for you to look at, would a READM.txt suffice to explain what I want you to look at? PPS I am having trouble finding the "Create your own ROI" tutorial page on the wiki. I know it exists, and that this is not described in it, though... thanks Stefan

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shared library error
by houman.ebrahimi 04 Jun '10

04 Jun '10

Hi, I am constantly getting the same error when running recon-all on different subjects: #@# Cortical ribbon mask Sat May 29 15:08:06 EST 2010 /home/houman/Desktop/freesurfer/subjects/PS2038/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance PS2038 mris_volmaskbin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux ubuntu 2.6.32-22-generic #33-Ubuntu SMP Wed Apr 28 13:28:05 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Sat May 29 15:08:07 EST 2010 I am running: freesurfer-Linux-centos4_x86_64-stable-pub-v.4.5.0-full.tar.gz i7 processor - Ubuntu 10.04 (Kernel Linux 2.6.32-22-generic, GNOME 2.30.0) I have referred to the suggested solutions at the following post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07975.html but neither seem to correct the problem. I am interested mainly in the data in the stats/aseg.stats file (which is generate on the step before the error). Is this error likely to affect the data in that file? Thanks! Houman

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Change LUT
by Bauer, Andrew J 03 Jun '10

03 Jun '10

Hi, There are two parts to my question, and they have to do with cortical parcellation color labeling: I'd like to change the look-up table such that some regions (in my case, ALL white matter) that are originally labeled with unique color codes, are DE-labeled (as in, are given no color). I know how to manually change the color codes in a text editor. However, I don't know how to change the LUT so that there is NO color label is attached. Second, if I edit the LUT, will the region colors be automatically updated when I view the regions, either surface or volume? Regards, Andrew

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Re: [Freesurfer] Freesurfer Digest, Vol 76, Issue 4
by Marietta, Jacquie R 03 Jun '10

03 Jun '10

Thanks:) Jacquie Marietta Research Assistant University of Iowa Hospitals and Clinics Department of Psychiatry W 292 GH Iowa City, Iowa 52245 319 353 8513 jacquie-marietta(a)uiowa.edu -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Wednesday, June 02, 2010 4:02 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 76, Issue 4 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: autorecon2 error (Gabriel Go.Es.) 2. Re: autorecon2 error (Bruce Fischl) 3. Re: autorecon2 error (Gabriel Go.Es.) 4. Re: autorecon2 error (Bruce Fischl) 5. label2label with two subjects directories (Garth Coombs) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Jun 2010 19:11:25 +0000 From: "Gabriel Go.Es." <gabriellbk(a)hotmail.com> Subject: Re: [Freesurfer] autorecon2 error To: <nicks(a)nmr.mgh.harvard.edu>, <reuter(a)mit.edu> Cc: free surfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <SNT124-W28C9EC56CF343A93A46AFADCD00(a)phx.gbl> Content-Type: text/plain; charset="iso-8859-1" Thank you I redownloaded the mri_ca_label file and worked, it seems that gets corrupted when donwloading, but now it appears a new error, from the autorecon2, any idea??? #@# Intensity Normalization2 Wed Jun 2 14:58:57 CEST 2010 /root/trabajo/freesurfer/subjects/T1_GE1/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... mri_normalize: aseg volume aseg.mgz must be conformed using MR volume brainmask.mgz to mask input volume... unconformed source detected - conforming... Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Jun 2 14:59:06 CEST 2010 Best, Gabriel _________________________________________________________________ ?Quieres conocer trucos de Windows 7? ?Los que ya lo usan te los cuentan! http://www.sietesunpueblodeexpertos.com/index_windows7.html

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Group analysis---qdec questions
by liyari5018 03 Jun '10

03 Jun '10

Hi FS experts, when i use qdec to analysis my data: 45 norms and 45 patients, what does this means: Is there a diagnosis--gender interaction in the mean thickness? (PS: I got a corrected results in this item, but i don't know how to report it) Thanks for you reply! LJ

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Freesurfer June 2010