Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

Re: [Freesurfer] Load Brodmann surface area into inflated surface
by _andreia_＠sapo.pt 23 Apr '12

23 Apr '12

(forgot to do answer all, here it goes for the list too) Citando _andreia_(a)sapo.pt: > Hi Bruce, > > The ideia is to show one control subject vs. one patient inflated > surface with BA surface (not volume, sorry) to show the difference > (reduced surface area in one patient). Loading the relevant labels > worked (I have the statistics shown in bar graphs, the images are > only for visualizing the difference between controls and patients). > When I threshold the labels in the subject's inflated surface they > shrink a lot, is this supposed to happen? > > The BA are V1, V2 and MT. What is the thresghold for V2? > > And is it correct to load ?h.sulc in a gray scale to have the usual > cortex representation, or I should do it other way? > > > And getting back to my previous email: > > Another question is, how is the volume of the BA calculated? Is it >>> from the surface-based stream? >>> >>> And, which surface area is the on in the output of the BA stats? Is it >>> the pial or wm? > > Thanks, > Andreia > > > Citando Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > >> Hi Andreia >> >> sorry, I don't understand. What do you mean when you say you want >> to " show the resulting Brodmann area (only 3 BA) volume in the >> inflated surface of my subjects". Do you mean just to show what >> portion of the surface is in each of 3 Brodmann areas? That you >> would do by loading the relevant labels, although you will probably >> want to threshold them differently (e.g. V1 you could threshold at >> .9 which is 90% and it would have about the surface area of an >> individual, while MT would need to be closer to .4 or .5). Or do >> you actually mean the volume of gray matter within each BA? If the >> latter, it's just 3 numbers/subject, so I would think you would >> want a scatter plot or something, not a map on the surface. >> >> cheers >> Bruce >> >> >> On Mon, 23 Apr 2012, _andreia_(a)sapo.pt wrote: >> >>> Hi all, >>> >>> I'm sorry if these questions have already been covered here, but I've >>> looked into the archives and still can't do what I need (and since I'm >>> running out of time for this task I decided to post here): >>> >>> I'm using version 5.0.0. >>> >>> I want to show the resulting Brodmann area (only 3 BA) volume in the >>> inflated surface of my subjects to show the differences between >>> patients and controls (for visualization purpose only). I've managed >>> to overlay the volume in the curvature menu but this is for the entire >>> cortex and I can't show the values bar. How can I show the volume of >>> only 3 BAs and have the scale bar? >>> >>> Another question is, how is the volume of the BA calculated? Is it >>> from the surface-based stream? >>> >>> And, which surface area is the on in the output of the BA stats? Is it >>> the pial or wm? >>> >>> Thanks in advance, >>> Andreia >>> >>> _______________________________________________ >>> 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.

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Neuroscience project, hippocampus segmentation
by Paweł Dembiński 23 Apr '12

23 Apr '12

Hi, I'm currently doing a project for my neuroscience course. I've decided to compare automatic segmentation methods (comparing hippocampus volumes) (using Freesurfer and FIRST). My question is, whether there is a set of commands in Freesurfer which will enable me to segment only hippocampus. I'm only intrested in volumes, nothing else. I've noticed that recon-all takes a lot of time and been wandering if there is a faster way. Pawel

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prefrontal cortex values
by Ahmed, F, Me <fahmed＠sun.ac.za> 23 Apr '12

23 Apr '12

Hello FS experts, A quick question for you all. Does the FS stream produce any values for the Prefrontal Cortex specifically? Thanks, Fatima ________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.

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surface does not match
by Righart, Ruthger Dr. 23 Apr '12

23 Apr '12

Dear Freesurfers, I analyzed a dataset with FS 5.1 but upon loading the data in tksurfer I get the following error: mrisReadTriangleFile(/.../surf/lh.sphere.reg): surface doesn't match /.../surf/lh.inflated The same error occurs when I run mris_preproc as a step before GLM analyses (mri_glmfit). A similar problem was described in the mailing list and offered the possibility to resolve this with the following command: recon-all -s subjid -make all This command only runs at the moment for a few of my subjects (I am at the moment waiting for the results of these analyses). For the majority of my subjects having the same error in mrisReadTriangleFile this command does not run. For those, it seems that the command -make all is not recognized. Does anyone know why it does not run or is there an alternative solution in FS 5.1. for this problem? Thank you very much in advance for your help! Ruthger Righart

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Load Brodmann surface area into inflated surface
by _andreia_＠sapo.pt 23 Apr '12

23 Apr '12

Hi all, I'm sorry if these questions have already been covered here, but I've looked into the archives and still can't do what I need (and since I'm running out of time for this task I decided to post here): I'm using version 5.0.0. I want to show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects to show the differences between patients and controls (for visualization purpose only). I've managed to overlay the volume in the curvature menu but this is for the entire cortex and I can't show the values bar. How can I show the volume of only 3 BAs and have the scale bar? Another question is, how is the volume of the BA calculated? Is it from the surface-based stream? And, which surface area is the on in the output of the BA stats? Is it the pial or wm? Thanks in advance, Andreia

2 1

Help Error running recon-all-s during installation test
by Eustratios Karavasilis 23 Apr '12

23 Apr '12

Dear all, I am new freesurfer user (version 5.0.0 installed to windows using virtual machine), during the installation i was trying to test the installation, following the recommended steps. The recon-all -s terminated with errors, andi can't find the bug. I send you the command line and the report including the error message to help you. ------------------------------------------------------ FREESURFER_HOME /home/virtualuser/freesurfer SUBJECTS_DIR /home/virtualuser/freesurfer/subjects ------------------------------------------------------------------ FreeSurfer:~> recon-all -s ernie -i $SUBJECTS_DIR/sample-001.mgz -i $SUBJECTS_DIR/sample-002.mgz -autorecon1 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/freesurfer/subjects/ernie mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz... /home/virtualuser/freesurfer/subjects/ernie mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/sample-002.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Mon Apr 23 04:55:18 EDT 2012 Found 2 runs /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /home/virtualuser/freesurfer/subjects/ernie mri_robust_template --mov /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz --average 1 --template /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001-iscale.txt /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002-iscale.txt --subsample 200 --lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz as movable/source volume. --mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz'... reading source '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz ) to TP 1 ( /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1.32812)mm and dim (256, 256, 128) Dst: (1, 1, 1.32812)mm and dim (256, 256, 128) Asserting both images: 1mm isotropic and (256, 256, 170) voxels Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels. Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels. Reslicing using trilinear interpolation Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels. Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels. Reslicing using trilinear interpolation Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 42 ) -- gpT ( 64 , 64 , 42 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0356683 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 0 ( -1 ), max sat: 8 ( 0.132346 ), sat diff: 8 -- Iteration: 3 trying sat: 4 min sat: 4 ( 0.391276 ), max sat: 8 ( 0.132346 ), sat diff: 4 -- Iteration: 4 trying sat: 6 min sat: 6 ( 0.21266 ), max sat: 8 ( 0.132346 ), sat diff: 2 -- Iteration: 5 trying sat: 7 min sat: 6 ( 0.21266 ), max sat: 7 ( 0.16739 ), sat diff: 1 -- Iteration: 6 trying sat: 6.5 - final SAT: 7 ( it: 6 , weight check 0.16739 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -0.0652797588760 0 1.0000000000000 0 0.2680379336344 0 0 1.0000000000000 0.4401045835282 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 3 S( 32 32 21 ) T( 32 32 21 ) Iteration(f): 1 -- diff. to prev. transform: 0.706674 Iteration(f): 2 -- diff. to prev. transform: 0.0752789 Iteration(f): 3 -- diff. to prev. transform: 0.0228908 Iteration(f): 4 -- diff. to prev. transform: 0.0664109 Iteration(f): 5 -- diff. to prev. transform: 0.0548568 max it: 5 reached! Resolution: 2 S( 64 64 42 ) T( 64 64 42 ) Iteration(f): 1 -- diff. to prev. transform: 0.192344 Iteration(f): 2 -- diff. to prev. transform: 0.0308604 Iteration(f): 3 -- diff. to prev. transform: 0.0187651 Iteration(f): 4 -- diff. to prev. transform: 0.00839767 < 0.01 :-) Resolution: 1 S( 128 128 85 ) T( 128 128 85 ) Iteration(f): 1 -- diff. to prev. transform: 0.128598 Iteration(f): 2 -- diff. to prev. transform: 0.0134286 Iteration(f): 3 -- diff. to prev. transform: 0.00837132 < 0.01 :-) Resolution: 0 S( 256 256 170 ) T( 256 256 170 ) Iteration(f): 1 (subsample 200) terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s ernie exited with ERRORS at Mon Apr 23 04:56:44 EDT 2012 FreeSurfer:~> which freesurfer /home/virtualuser/freesurfer/bin/freesurfer -------------------------------------------------------------------------------------------------------------------------------- Thanks in advanced, Stratos

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improving automated cerebellar parcellation
by Anthony Dick 23 Apr '12

23 Apr '12

Hello, I developed a new atlas for parcellating the cerebellum, based on 20 brains manually segmented by Jörn Diedrichsen, which he was kind enough to share (note these also formed the basis for his 2009 paper in Neuroimage (46; 39-46). I got the segmentation to work, but I would not say it works well. As you can see from the attached image, it is not ready for prime-time. On the left is the brain of subject 1, manually segmented. On the right is the brain of the same subject with the automated sementation, based on the developed atlas. My question is, how can I improve it? I realize this is an open question and potentially difficult to answer without some probing, but this is a resource I think a lot of users would like to have access to, so perhaps it is worth the effort. Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick Lab Webpage: http://dcn.fiu.edu

2 6

Definition of Surface Area Metric
by Dhinakaran Chinappen 22 Apr '12

22 Apr '12

Dear Freesurfer Experts, Would you mind clarifying what the measure of surface area anatomically means? Is it the area of the pial surface? Thanks in advance, Dhinakaran.

2 1

Another -use-gpu experiment
by Burns, Scott S 20 Apr '12

20 Apr '12

Freesurfers, I'd like to add my two about a recent experiment I ran with recon-all -use-gpu. (I'm using v5.1) I took 6 T1 scans, imported them into two subjects a piece (gpu_SUBJID, cpu_SUBJID) and ran 'recon-all -all -use-gpu' on the gpu_ subject and the normal 'recon-all -all' on the cpu subjects. All gpu subjects ran on a single GTX 480. On average, I saw about a 16% speedup using GPU hardware, which translates to about 4 hours on the hardware I'm using. Qualitatively, the final inflated surfaces and {w,g}m boundaries are very similar. Two questions: 1) Would you recommend -use-gpu for "production" analyses using FS v5.1? 2) Separately from the above experiment, I ran one gpu subject using 4 GTX 480s and saw no significant time difference. Is this to be expected, ie your CUDA code doesn't scale across multiple GPUs? Just curious, certainly not a deal-breaker if it doesn't. Thanks for your input. Scott Burns Neuroimaging Analyst Education and Brain Science Lab Kennedy Center Vanderbilt University

2 1

-clean
by Joshua Lee 20 Apr '12

20 Apr '12

If I were to want to re-run a recon-all completely fresh on a subject, what do I need to do aside from creating a new subject directory? I had previously thought that by adding the -all flag, all old files would be over written (i.e. overwrite with a new brainmask.mgz). I want everything fresh. Does the -clean flag do it all? Thanks Josh

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Freesurfer April 2012