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30085 discussions

ROI based on Talairach coordinate
by Ben Hamida Cammoun Leila Faiza 16 Feb '10

16 Feb '10

Dear Freesurfer users and experts, This is my second attempt :( I am trying to construct a roi based on some talairach coordinate coming from a paper, but I completely fail to do it with matlab and neither manually with tksurfer. My first try was to use the transformation Talairach.xfm with matlab, inverse it and try to recover RAS coordinate, it gives me completely wrong values. Second try was to introduce the Tal coordinate directly in Tksurfer, which is not possible I think (correct me if I am wrong), with the version I have the is a bug in tkmedit I guess when introducing Talairach coord (the ideas was to save them and to load the vertex in tksurfer).. the values changes in the edit box.. Is there another way?? Is it possible with script? Or how to do this by matlab? Please don't ignore the request. Leila

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tractography and freesurfer
by Dana W. Moore 16 Feb '10

16 Feb '10

I have a colleague who is interested in the DTI toolkit to coregister DTI results with FreeSurfer's segmentation. Is that available in any form yet? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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Gyrification index for individual regions
by Lena Palaniyappan 16 Feb '10

16 Feb '10

I managed to obtain outputs from recon-all lGI now I would like to obtain a mean gyrification index (not sure if the mean is meaningful?!) for all vertices within 3 ROIs as defined by Destrieux atlas - How should I do this? Can I treat lGI surfaces just as thockness maps in which case can I use mri_segstats to obtain mean values? Cheers Lena This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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mris_anatomical_stats error
by yzhangd＠artsci.wustl.edu 16 Feb '10

16 Feb '10

Dear experts, i try to run the command mris_anatomical_stats to get GrayVol, ThickAvg, etc from the left cortex as following: mris_anatomical_stats -l lh.cortex.label -f nmr033_2/stats/lh.cortex.stats nmr033_2 lh so the output is like following and did not generate any stats file(lh.cortex.stats) : limiting computations to label lh.cortex.label. reading volume /windata/yuning/freesurfer/nmr033_2/mri/wm.mgz... reading input surface /windata/yuning/freesurfer/nmr033_2/surf/lh.white... reading input pial surface /windata/yuning/freesurfer/nmr033_2/surf/lh.pial... reading input white surface /windata/yuning/freesurfer/nmr033_2/surf/lh.white... /windata/yuning/freesurfer/nmr033_2/label/lh.cortex.label /windata/yuning/freesurfer/nmr033_2/label/lh.cortex.label Segmentation fault could anyone tell me what's wrong with it and what segmentaion fault is ? thanks a lot yuning

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question abt mri_vol2surf....
by Ritobrato Datta 16 Feb '10

16 Feb '10

Hello All, I have a simple question. I have functional data (3 mm cubic voxels) from 20 subjects that I am using mri_vol2surf to resample on the fsaverage surface. I want to run qdec or mri_glmfit on these data. In order to do grp stats with functional data, what surface do I need to specify in the '--surf' flag ? Does it matter ? Thanks Ri

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recon-all -s $subject -make all
by Alessandro D. Gagliardi 16 Feb '10

16 Feb '10

Hello FreeSurfers, recon-all -make is working now, but it's taking as long as it did the first time I ran it. I originally ran "recon-all -s cb -i CB_anat+org.BRIK -i CB_anat2+orig.BRIK -all" (for example) back in May and haven't messed with the results except for generating some label files with mri_annotation2label. I deleted the original BRIKs, but I don't see why that would matter in this case since the orig.mgz files are still there. Is it taking so long because so much has changed between 4.3 and 4.5, or is something wrong? Thanks, Alessandro D. Gagliardi Ph.D. Candidate Integrative Neuroscience Program Rutgers University Mind Brain Analysis adfgagliardi(a)gmail.com P.S. To generate a2009s annotations files for fsaverage, do I just run "recon-all -s fsaverage -make all"? On Sat, Feb 13, 2010 at 4:28 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Alessandro, > > usually that means that the smoothwm is out of date with the sphere.reg. > You can run mris_euler_number on both to make sure they have the same number > of vertices, faces and edges. Or you can just run > > recon-all -s $subject -make all > > which will rebuild things if it needs to >

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Wmparc Destrieux atlas
by Lena Palaniyappan 16 Feb '10

16 Feb '10

Hi all Could anyone help me with extracting the wmparc volume stats in accordance with Destrieux atlas? As it stands now the segmentations corresponding to whitematter beneath Destrieux 2009 parcellations are returned empty when called for Many thanks Lena \_________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Longitudinal processing clarification
by Derin Cobia 16 Feb '10

16 Feb '10

(Questions for all, but maybe more directed towards Martin) I have some questions about manual edits in regard to the longitudinal stream. Based on the current info on the wiki page, it appears that no edits are pushed forward from the cross-sectional (initial) runs of the subject data, as any information on the *.long.* runs come from the template. However, I've noticed that WM edits and surfs from the template are used in for the *.long.* processing. In essence, my question is when/where should manual edits (i.e., control points, WM, pial edits) occur when conducting longitudinal processing in 4.5? It seems I remember that in 4.3 edits in the cross-sectional work would be pushed forward to the *.long.* images, but such is not the case anymore (?). Are edits to occur in the template (i.e., 'base') now, or in the *.long.* runs? Thanks. -Derin

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a question about rebuild_gca_atlas.csh
by Guang Zeng 15 Feb '10

15 Feb '10

Hi, there, I am using the rebuild_gca_atlas.csh to build our own subcortical atals now, and met a problem at the second step which is # Train using ONE_SUBJECT, the command line is: mri_ca_train -prior_spacing 2 -node_spacing 8 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_man.xfm -T1 norm.mgz -check $OneID /data1/radiology/m047599/temp_fs_2/freesurfer-v4.5.0/subjects/average/RB_12-Feb-2010.gca and it gave me errors such as; ERROR: Left_Caudate: 104 167 182, tal *** x=22.896236 > 5 ***, y=33.105412, z=-16.869007 ERROR: Left_Caudate: 104 167 183, tal *** x=22.900818 > 5 ***, y=34.053909, z=-16.893997 ERROR: Left_Caudate: 104 167 184, tal *** x=22.905401 > 5 ***, y=35.002407, z=-16.918985 ERROR: Left_Caudate: 104 167 185, tal *** x=22.909985 > 5 ***, y=35.950901, z=-16.943975 ERROR: Left_Caudate: 104 167 186, tal *** x=22.914564 > 5 ***, y=36.899403, z=-16.968966 ERROR: Left_Caudate: 104 167 187, tal *** x=22.919147 > 5 ***, y=37.847897, z=-16.993954 ERROR: Left_Caudate: 104 167 188, tal *** x=22.923729 > 5 ***, y=38.796391, z=-17.018944 Why it will have an error related to Left_Caudate? Is the FreeSurferColorLut.txt file called somewhere ? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469226/direct/01/

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mris_ca_label: could not read surface file
by Alessandro D. Gagliardi 15 Feb '10

15 Feb '10

Dear Freesurfers, I just upgraded to the latest version of Freesurfer (leopard-i686-stable-pub-v4.5.0) and I want to rerun mris_ca_label to generate ?h.aparc.a2009s.annot files. I figured I would just run the command described at http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable, namely: mris_ca_label -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs label/?h.aparc.a2009s.annot but when I do so, I get the following error: mris_ca_label: could not read surface file /Users/adfgagliardi/Documents/Lab/subjects/hj/surf/?h.smoothwm for hj No such file or directory surf/?h.smoothwm does exist for hj, so I don't know why it says "No such file". I tried regenerating it using mris_smooth -n 3 -nw ?h.white ?h.smoothwm which completed without error, but mris_ca_label continues to say that it cannot read ?h.smoothwm Any help would be greatly appreciated. Alessandro D. Gagliardi Ph.D. Candidate Integrative Neuroscience Program Rutgers University Mind Brain Analysis adfgagliardi(a)gmail.com

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