Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

Rejoindre mon réseau sur LinkedIn
by Mohan Boddu via LinkedIn 27 Sep '11

27 Sep '11

LinkedIn ------------ Mohan Boddu souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Mohan Boddu http://www.linkedin.com/e/-qq80um-gt2xlltn-6h/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Mohan Boddu http://www.linkedin.com/e/-qq80um-gt2xlltn-6h/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Mohan Boddu ? Les contacts de Mohan Boddu consulteront votre profil : Votre arrivée dans le réseau de Mohan Boddu attirera l'attention d'autres membres de LinkedIn. Voir qui a consulté votre profil. http://www.linkedin.com/e/-qq80um-gt2xlltn-6h/wvp/inv18_wvmp/?hs=false&tok=… -- (c) 2011, LinkedIn Corporation

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mri_convert error
by Andries R. Van Der Leij 27 Sep '11

27 Sep '11

Dear FS team, I'm working on some NIFTI images which I want to convert to mgz. When I try to do this, I get: mri_convert /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/NIFTI/sc0219-20101101-0003-T13DTFESENSE.nii.gz /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/FREESURFER/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/NIFTI/sc0219-20101101-0003-T13DTFESENSE.nii.gz... WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent (1,1) (1,1) (1,1.6) This is probably due to shear in the vox2ras matrix Input Vox2RAS ------ 0.013 0.018 1.600 -125.223; -1.000 -0.001 0.020 158.408; -0.002 1.000 -0.029 -85.678; 0.000 0.000 0.000 0.000; TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.012721, -0.999918, -0.00162597) j_ras = (0.0180632, -0.00139604, 0.999836) k_ras = (0.999756, 0.0127483, -0.0180439) writing to /home/avdleij1/ID1000/ID1000_scans/CON_ID1000/FREESURFER/mri/orig/001.mgz... I'm not sure what's going on here, but I assume that something isn't right in the matrix, as my data (Phillips par/rec converted to NIFTI) are 1*1*1 mm (see below). I assume that our local conversion app does something fishy with the matrix. I'm completely in the dark on how to solve this. Any ideas would be greatly appreciated! Best, Andries avdleij1@debian:~/ID1000/ID1000_scans/CON_ID1000/NIFTI$ fslhd sc0219-20101101-0003-T13DTFESENSE.nii.gz filename sc0219-20101101-0003-T13DTFESENSE.nii.gz sizeof_hdr 348 data_type FLOAT32 dim0 3 dim1 256 dim2 256 dim3 160 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 16 nbyper 4 bitpix 32 pixdim0 0.0000000000 pixdim1 1.0000000000 pixdim2 1.0000000000 pixdim3 1.0000000000 pixdim4 1.0000000000 pixdim5 0.0000000000 pixdim6 0.0000000000 pixdim7 0.0000000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 0.012721 0.018063 0.999756 -125.222908 qto_xyz:2 -0.999918 -0.001396 0.012748 158.408218 qto_xyz:3 -0.001626 0.999836 -0.018044 -85.677658 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Anterior-to-Posterior qform_yorient Inferior-to-Superior qform_zorient Left-to-Right sform_name Aligned Anat sform_code 2 sto_xyz:1 0.012721 0.018063 1.599609 -125.222908 sto_xyz:2 -0.999918 -0.001396 0.020397 158.408218 sto_xyz:3 -0.001626 0.999836 -0.028870 -85.677658 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Anterior-to-Posterior sform_yorient Inferior-to-Superior sform_zorient Left-to-Right file_type NIFTI-1+ file_code 1 descrip FSL4.1 aux_file

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thickness_clinical_correlations
by Rajagopalan, Venkateswaran 26 Sep '11

26 Sep '11

Dear All, I am trying to correlate clinical disability measure ALSFRS score with cortical thickness in ALS patients. Attached is the fsgd file. I am not able to run mris_preproc with this fsgd file what am I doing wrong here, also my design matrix contrast is 1 0 am I right. I am interested in seeing whether there any correlation between cortical thickness changes in ALS patients with their ALSFRS score. Thanks Venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Re: [Freesurfer] using isxconcat-sess for partial correlation coefficient map
by Douglas N Greve 26 Sep '11

26 Sep '11

Add "-m pcc" to the command line doug SHAHIN NASR wrote: > Hi, > > Would you tell me how can I use isxconcat-sess to calculate group > averaged "partial correlation coefficient map"? I have already > generated pcc.nii files for each individual subject. > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > -- 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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QDEC results and stats
by carolina.mr 26 Sep '11

26 Sep '11

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using isxconcat for partial correlation coefficient map
by SHAHIN NASR 26 Sep '11

26 Sep '11

Hi, Would you tell me how can I use isxconcat-sess to calculate group averaged "partial correlation coefficient map"? I have already generated pcc.nii files for each individual subject. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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volume of different lobes of the brain....
by Gonzalo Rojas Costa 26 Sep '11

26 Sep '11

Hi: How can I get the volume of the different lobes of the brain (occipital, parietal, temporal, etc) ?... White matter and gray matter?... Labels ?... Sincerely, Gonzalo Rojas Costa

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Tracula references
by Shanqing Cai 26 Sep '11

26 Sep '11

Hi, I am using Tracula in my diffusion data analysis and am interested in finding out what would be the best citations or references for this tool. A quick Internet search brings me to two conference papers, one in ISMRM and one in an IEEE conference. Are there any journal articles that have been published on Tracula? I need the information for better understanding of the tool and possible citations in future publications. Thank you. Best regards, Shanqing Cai

2 1

26 Sep '11

Hello, I was wondering what orientation conventions are used when calculating the affine transformation matrix in register.dat. For an example, I'll use the data from subject 101 of the fsfast tutorial. According to mri_info, the functional volume is in LPS orientation, and the processed anatomical volume (T1.mgz) is in LIA orientation. Does the matrix in register.dat convert from the functional LPS orientation to the anatomical LIA orientation, or does the matrix assume these volumes are already transformed in some other way? Thanks, Clark

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Talairach registration failes
by Martijn Steenwijk 26 Sep '11

26 Sep '11

Dear all, I have a problem running Freesurfer on images having a relatively tight FOV. While running talairach_afd, the registration of the template to the image fails. Checking the registration (as explained on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach) reveals that the template gets completely squeezed, so it's not a problem of a too sensitive registration quality detection, it's the registration which fails. Is there a way to make this registration more robust for these kind of images? With best regards, Martijn

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Freesurfer September 2011