Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

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

2 1

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

2 1

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

2 2

Brainmask.nii Reading
by Nooshin Zadeh 20 Apr '12

20 Apr '12

Dear FS friends I need to do skull stripping of MRI images, and for this purpose I have used FS. For reading the data from "brainmask.mgz", I converted it to "brainmask.nii". Can you please tell me how can I read the data from "brainmask.nii" is MATLAB? Do you know other way of reading the data from brainmask.mgz? I am looking forward to hear from you. Thanks in advance -- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

2 1

long_qdec_table error
by Derin J Cobia 20 Apr '12

20 Apr '12

Martin, I'm getting the following error when running long_qdec_table: ========= [derin@otis ccnm_mprage_v4.5_long]$ long_qdec_table --qdec qdec/ccnm_prog_30_long_Th.qdec.table.dat --cross --out qdec/ccnm_prog_30_long_Th.cross.qdec.table.dat Parsing the qdec table: qdec/ccnm_prog_30_long_Th.qdec.table.dat Traceback (most recent call last): File "/pkg/brainmap/freesurfer-v5.1.0/bin/long_qdec_table", line 142, in ? longqdec = LongQdecTable(options.qdec) File "/pkg/brainmap/freesurfer-v5.1.0/bin/LongQdecTable.py", line 30, in __init__ self.parse(stpmap) File "/pkg/brainmap/freesurfer-v5.1.0/bin/LongQdecTable.py", line 58, in parse if strlst[0].upper() == 'SUBJECTS_DIR': IndexError: list index out of range ========= I haven't had much luck troubleshooting it, maybe I have too many numerical variables in the table? I guess I could always reconstruct it by hand, but wondering if you had any thoughts, thanks. FS v5.1.0 CentOS 4 -Derin

1 0

Re: [Freesurfer] WM modification
by Gabriel Gonzalez Escamilla 20 Apr '12

20 Apr '12

1 0

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