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19 participants
30132 discussions

re-calculating stats based on an updated ?h.pial surface
by Dominic Brendon Dwyer 15 Oct '10

15 Oct '10

Hi all, We're using a tool which allows direct alteration of the pial surface (http://sites.google.com/site/vxxsoftware/) resulting in another ?h.pial file being created. We've found that it is a good way to both decrease and increase the pial boundary where there are errors. The current procedure is to use mris_fill once the surfaces are created and then apply this to the brainmask.mgz before re-running recon2. I was wondering if it was possible to recalculate the surface stats based on an altered ?h.pial file without running recon2 again? The reason being is that if the surface is extended rather than reduced then it will not necessarily appear in the updated pial surface. Any help would be greatly appreciated. Many thanks, Dominic Melbourne Neuropsychiatry Centre

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Cannot allocate memory
by Pradeep 14 Oct '10

14 Oct '10

Hello All, I get the following error while running mri_glmfit. I am using freesurfer V5.0. But qdce seem to run well with the similar settings. ---------log------- [pthiyyagura@ fsgd]$ mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd --C group.diff.mtx gdfReadHeader: reading g2v0.fsgd INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /data/rawdata/API/FS_MPRAGE/fsgd cmdline mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd --C group.diff.mtx sysname Linux hostname machine x86_64 user pthiyyagura FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh logyflag 0 usedti 0 FSGD g2v0.fsgd glmdir g2v0 IllCondOK 0 DoFFx 0 Creating output directory g2v0 Loading y from /data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh MRIalloc: could not allocate 1378828612 slices Cannot allocate memory --------end------- Any suggestion on this would be greatly appreciated. Thanks, Pradeep

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MNI152
by Yigal Agam 14 Oct '10

14 Oct '10

Hi, Is it possible to export a functional volume from individual brain space to mni152, so it can be overlaid on the standard mni152 brain in fslview? Thanks, Yigal

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Problem with intensity normalization
by Huo, Jing 14 Oct '10

14 Oct '10

Hi, I have a problem with using mri_normalize for intensity normalization for T1w+contrast 3D volumes. What I ran: mri_convert t1.hdr t1.mgz mri_normalize -g 1 t1.mgz t1_norm.mgz mri_convert t1_norm.mgz t1_norm.hdr (1) The first problem is that all volumes are 256*256*256 as output. Why are there dummy slices? Is there an automatic way to get rid of the dummy slices? (2) For 1/3 of the 50 cases, I observed a spatial shift for some voxels. I was wondering whether this comes from the spatial registration, but it is wierd coz the rest 2/3 of the cases are pretty OK visually. Anyone has similar experience before? That would be very helpful. Thanks. (3) For 4 cases, the brain white matter was normalized to 59 instead of 110. I dunno why... Thanks! I will really appreciate if anyone could help here! Best, Jing IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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FDR in gray matter
by Yigal Agam 14 Oct '10

14 Oct '10

Hi, Is it possible to restrict FDR correction to gray matter in tkmedit? Thanks

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postdoctoral fellow position for dementia research
by Anqi Qiu 14 Oct '10

14 Oct '10

Postdoctoral Fellow Position on Dementia NeuroImaging Job description: National University of Singapore (NUS) is a leading global university centred in Asia. It offers a global approach to education and research, with a focus on Asian perspectives and expertise. Computation functional anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and cognition studies using neuroimaging techniques. Our group is leading the dementia neuroimaging project in Singapore. The project involves multi-modal MRI techniques, including resting fMRI, HARDI, and ASL. We are looking for a research fellow who is interested in multi-modal MRI studies in dementia, especially, who is interested in developing anatomical and functional connectivity methods or investigating anatomical and functional connectivity in dementia. We offer high salary with medical and other benefits. Requirements: Ph. D or MD Background on Alzheimers disease or vascular disease research is preferable but necessary Knowledge in statistical analysis is necessary Good communication and writing skills in English language If you are interested in the jobs listed below, please send your CV to Dr. Anqi QIU Division of Bioengineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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postdoctoral fellow position for dementia research
by Anqi Qiu 14 Oct '10

14 Oct '10

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Mapping labels to the RH on Macs
by Tessa Harrison 14 Oct '10

14 Oct '10

Dear FreeSurfers, I am running FS 4.5 or FS 5.0 on Mac OS X 10.6.4 -Intel (see attached screenshot). I am not able to map RH labels created in fsaverage to the RH of any of my subjects. LH labels map to the LH from qdec "Map Label to All Subjects" option and from the command line with no problem. However, when I try to map RH labels (that map correctly to the RH in fsaverage) to individual subjects, the command appears to work (no error messages), but something goes wrong. It appears that the label is actually mapped to the LH because when I pull it up on the RH in an individual subject it looks like scattered dots (see attached image). The same thing happens on another Mac in our lab. I have tried both FS 4.5 and 5.0 and the problem occurs in both versions. Could this be a bug in the Mac FS release? I did not find any mention of this problem in the archives. Thank you for you help! -Tessa

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converting IMA files
by Lisa F. Akiyama 14 Oct '10

14 Oct '10

Hello, I am a Freesurfer newbie trying to use the mri_convert command to convert IMA format files to either nii or nifti1 format files. Whenever I run the command I get an error at the very end saying that it failed to write (please see below for the exact output error that was displayed). Any help would be greatly appreciated. Thank you in advance. Best, Lisa Akiyama % mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nii -o 393-2-4.nii mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot nii > -o 393-2-4.nii $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima... rows = 256 cols = 256 TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to 393-2-4.nii... niiWrite(): error opening file 393-2-4.nii ERROR: failure writing 393-2-4.nii as volume type 24 % mri_convert -i $SUBJ_DIR/393-2-4.ima -ot nifti1 -o 393-2-4 mri_convert -i /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima -ot > nifti1 -o 393-2-4 $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /Volumes/Elements/adult_brain/k_h/slices/393-2-4.ima... rows = 256 cols = 256 TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to 393-2-4... nifti1Write(): error opening file 393-2-4.hdr ERROR: failure writing 393-2-4 as volume type 20

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talairach transform error...
by Gonzalo Rojas Costa 13 Oct '10

13 Oct '10

Hi: I tried to process the T1 of a 7 month old patient with a big resection (see attached image)... I got the error: "#@# Talairach Failure Detection Wed Oct 13 13:21:39 CLST 2010 /usr/local/freesurfer/subjects/rivas_carmona_gabriel_13_10_2010/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux image 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Oct 13 13:21:39 CLST 2010" How can I process it ?... Sincerely, Gonzalo Rojas Costa

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