Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Mixing fs 4.3.1 with fs 4.5.0 longitudinally
by Jeff Sadino 15 Jul '10

15 Jul '10

Hello, I processed a 200 subject dataset cross-sectionally using fs 4.3.1 with the intention of running them longitudinally. I now read that the longitudinal stream in 4.3.1 is biased towards the initial timepoint and the 4.5.0 is the recommended version to do longitudinally. Can I just send my 4.3.1 subjects into the 4.5.0 longitudinal stream, or will I have have to redo the cross-sectional reconstruction in 4.5.0? Thank you very much, Jeff Sadino

2 1

A region loss in the ?h.aparc.stats
by liang wang 15 Jul '10

15 Jul '10

Hi, My freesurfer version is v4.5.0. Using tksurfer, I can find the corpus callosum shown in the ?h.aparc.annot (e.g., .. -annot aparc.annot). Moreover in the FreeSurferColorLUT.txt, this region exists (e.g. #No. 1004 ctx-lh-copuscallosum). However, I am surprised when finding its loss in the ?h.aparc.stats file. For all subjects, I did not find any morphometric measures of this region. Also, when using tksurfer to present ?h.aparc.annot, I can not find the insula in the displayed surface, though this region is existing in the ?h.aparc.stats and the FreeSurferColorLUT.txt (e.g. #No. 1035 ctx-lh-insula). I am creating a figure to show all these ROIs. Hence I am curious why there is not the insula shown. I am appreciated if anyone could give me a hand for solving this seemly conflicting information. Thanks so much. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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mri_ca_normalize hanging on a case
by Diandra Lucia 15 Jul '10

15 Jul '10

Hi there, We're processing some new 3T cases in FreeSurfer, and one case has been hanging just after it begins mri_ca_normalize: #@# CA Normalize Wed Jul 14 17:16:05 EDT 2010 /home/pnlstaff/freesurfer/subjects/case01264/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /share/apps/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 '/share/apps/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=29.9 skull bounding box = (62, 68, 28) --> (193, 185, 208) using (106, 107, 118) as brain centroid... mean wm in atlas = 107, using box (90,93,96) --> (122, 121,140) to find MRI wm before smoothing, mri peak at 164 after smoothing, mri peak at 163, scaling input intensities by 0.656 scaling channel 0 by 0.656442 using 244171 sample points... INFO: compute sample coordinates transform 1.058 0.020 -0.013 -10.456; -0.017 1.106 0.142 -38.892; 0.017 -0.123 0.973 10.525; 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 (125, 70, 32) --> (190, 174, 202) It doesn't give an error, it just hangs there, using 99.9% of the CPU. I checked the original T1 nifti and the brainmask and they look fine (we actually pre-skullstrip our T1s and copy them to create our brainmasks, and include -noskullstrip when we run autorecon-1). We're running these on freesurfer-Linux-rh9-stable-pub-v4.2.0. We actually had a similar problem about a year ago, and you sent us the CentOS4 build of the mri_ca_normalize script which fixed it, but my colleague who downloaded it from you is on vacation for 2 weeks and then is leaving, and I think it's locked up in her login. So, if this turns out to be a good solution again, I'd need to download the file again. Thanks for your help, Diandra -- Diandra Lucia Research Assistant Project Coordinator INTRuST Neuroimaging Leadership Core Psychiatry Neuroimaging Lab, BWH 1249 Boylston St., Boston, MA 02115 email: diandra(a)bwh.harvard.edu phone: 617-525-6118 cell: 602-332-7013

2 1

FDR Calculations
by James Porter 15 Jul '10

15 Jul '10

Hello- Does the built-in FDR function in tksurfer and QDEC run the calculations upon the actual values in the .mgh files, or does it take the exponent of those -log10(p) values first? -- Jim Porter, M.A. Graduate Student Clinical Science& Psychopathology Research University of Minnesota

2 1

problem converting .ima files
by Scott Hayes 15 Jul '10

15 Jul '10

Hi, I am trying to convert .ima files, and my command seems to work fine for some series: >mri_convert -it siemens -ot nii 523-2-4.ima ../srs2.nii but not others: >mri_convert -it siemens -ot nii 523-3-132.ima ../srs3.nii These are series collected from the same scan session. The data were reportedly collected at MGH: Siemens Allegra, around the fall of 2001 (if that helps at all). I'm running freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 I don't receive any error messages. The problem seems to be similar to one previously described in the archives, although I was not able to find the final solution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00890.html Any guidance would be appreciated. Thanks, Scott -- Scott M. Hayes, Ph.D. Memory Disorders Research Center Neuroimaging Research Center VA Boston Healthcare System Assistant Professor Department of Psychiatry Boston University School of Medicine

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Pial edits?
by Kolody, Brianna 15 Jul '10

15 Jul '10

2 1

different rotation matrix from same DICOM
by Xu, Jun 15 Jul '10

15 Jul '10

Hi, I found out something that I do not understand when I was trying to create rotation matrix from scratch. I have used two methods and hope they will give me the same results. 1st method---form matrix from cross product as described in http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_p… for example: -0.9994 0 0.0343 0.0153 -0.8953 0.4451 0.0307 0.4454 0.8948 I use formed rotation matrix * D (voxel size) --- I got exactly same affine matrix (1:3) as the one in nifti header. However, I tried another method since I would like to use normal vector if there is no row and col vector directly available in DICOM header. 2nd method --- form matrix from vox2ras_rsolveAA.m I got the matrix has the wrong signs although the numbers are exactly same. It cannot be simply apply some (making sensed) unity matrix for the correction (I have already correct normal vector for the sake of the requirement in 1st method ---- reverse the sign for the first 2 row in normal vector, if I do not correct it, the matrix is still not same). For example: 0.9994 -0.0000 0.0343 -0.0153 -0.8953 0.4451 -0.0307 0.4454 0.8948 I was wondering if you would know the reason for it. Thanks, Jun

2 1

Re: [Freesurfer] iPhone app
by Bruce Fischl 14 Jul '10

14 Jul '10

Hi All, I wanted to draw your attention to a new iPhone app that uses FreeSurfer segmentations written by Pedro Paulo de Magalhães Oliveira Junior. You can get it at; http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… I think surfaces are coming in future versions, and PPJ (ccd) welcomes comments and suggestions. cheers, Bruce

1 0

selxavg-sess with number of conditions error
by Gabriel A. Tobon 14 Jul '10

14 Jul '10

Hello, I have event related data with 69 different conditions, and every condition does not appear in every run. This causes selxavg-sess to throw an error. Part of the relevant debug output is below. Why does every condition need to appear in every run? Thank you, Gabe echo "$sess " | & tee -a $LF echo /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab date | & tee -a $LF date tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log Wed Jul 14 18:10:48 EDT 2010 if ( ! -d $sess ) then if ( ! -d /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab ) then set funcdir = $sess/$fsd set funcdir = /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold set anadir = $sess/$fsd/$analysisname set anadir = /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold/mc_analyze if ( $#OutParent == 0 ) then if ( 0 == 0 ) then set anadir = $sess/$fsd/$analysisname set anadir = /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold/mc_analyze else else echo anadir = $anadir | tee -a $LF echo anadir = /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold/mc_analyze tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log anadir = /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold/mc_analyze if ( -e $anadir && $DoGLMFit ) then if ( -e /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/data/kan_ecev_207ab/bold/mc_analyze && 1 ) then echo "analysis $analysis alread exists for $sessbase" | tee -a $LF echo analysis mc_analyze alread exists for kan_ecev_207ab tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log analysis mc_analyze alread exists for kan_ecev_207ab if ( $Skip == 0 && $Overwrite == 0 && ! $monly && ! $perrun && ! $jkrun ) then if ( 0 == 0 && 0 == 0 && ! 0 && ! 0 && ! 0 ) then echo "ERROR: analysis $analysis already exists. You must " | tee -a $LF echo ERROR: analysis mc_analyze already exists. You must tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log ERROR: analysis mc_analyze already exists. You must echo " specify whether to -skip or -overwrite" | tee -a $LF echo specify whether to -skip or -overwrite tee -a /mindhive/nklab/projects/eightcat-cluster/gtobon_analysis/8cat-ev2-final/analysis/log/selxavg3-sess-bold-mc_analyze-100714181048.log specify whether to -skip or -overwrite exit 1 ; exit 1

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creating binary masks for any given structure in aseg.mgz or aparc+aseg.mgz
by Mehul Sampat 14 Jul '10

14 Jul '10

Hi Folks, I would like to create binary masks for any given structure in aseg.mgz and aparc+aseg.mgz. I would then also like to map the masks back to native space. I think, I should use mri_binarize followed by mri_convert as shown in the two examples below: Example 1: a. mri_binarize --i mri/aseg.mgz --match 10 --o deep-gm-rois/lh-thalamus.mgz b. mri_convert -rl mri/orig/001.mgz -rt nearest deep-gm-rois/lh-thalamus.mgz deep-gm-rois/lh-thalamus.nii Example 2: a. mri_binarize --i mri/aparc+aseg.mgz --match 1022 --o ctx-gm-rois/lh-postcentral.mgz b. mri_convert -rl mri/orig/001.mgz -rt nearest ctx-gm-rois/lh-postcentral.mgz ctx-gm-rois/lh-postcentral.nii Ques 1: Is the best approach for this task ? I noticed in the FAQ that mri_vol2vol is recommended for conversion from freesurfer space to anantomical space. Ques 2: Is it better to use mri_vol2vol than mri_convert with the reslice option ? Thanks Mehul

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