Freesurfer October 2011

freesurfer@nmr.mgh.harvard.edu

95 participants
160 discussions

Table for aparc+aseg
by Shigetoshi Takaya 07 Oct '11

07 Oct '11

Dear FreeSurfers, In aparc+aseg file, each segmented or parceled region seems to be labeled by its own intensity (e.g. the intensity is 53 in the right hippocampus, 10 in the left thalamus...) when I see it on FSL viewer. Where can I find the table that shows the relationship between the intensity and the name of brain region? I want to extract the specific brain regions (e.g. parahippocampal gyrus, fusiform gyrus...) from the result of aparc+aseg, and use them for the seed mask or the termination mask in structural connectivity analysis (tractography). I appreciate your help. Thank you, Shige

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retinotopy analysis description
by Michelle Umali 07 Oct '11

07 Oct '11

Dear Freesurfers, I am trying to describe how freesurfer conducts it's retinotopy analysis to make the polar, eccen and fieldsign maps. Is there a detailed description of this somewhere? I can't seem to find an indepth description on the wiki. Thanks. Michelle

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Cut plane feature in tksurfer
by Jodie Davies-Thompson 07 Oct '11

07 Oct '11

Dear FreeSurfers, I am following the cut plane steps on the freesurfer wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch) I marked a closed areas, press the 'cut closed line' button, left-click in the area, and then press the 'fill uncut area' button. Upon clicking this last button, tksurfer crashes and the below error appears. tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. Abort I've seen two other posts with the same problem (links below), but no solution. Can anyone advise on this? Regards, Jodie http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14612.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16303.html -- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology& Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC Canada V5Z 3N9 Tel: 604-875-411 ext 69003

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cwp and QDEC color scale
by Antonella Kis 07 Oct '11

07 Oct '11

Hello Surfers, I would appreciate if you can help me with the following question: what should be the range values on the QDEC and/or GLM color scale if the cwp values for the cached clusters at thresh 2 and cwpvalthresh .99 are between 0.4465 and 0.9710? Many thanks. AK

1 2

Process monkey data
by Pedro Paulo de Magalhães Oliveira Junior 07 Oct '11

07 Oct '11

I have data from 100 monkeys and I need to compare cortical thickness among two groups. In the wiki page there is an entry MonkeyData that has a set of scripts which break-down the steps needed, unfortunately I'm having trouble with this scripts and FS 5.1 Are there an updated version of those procedures? Thanks PPJ -- iOS 5.0

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Resampling NIFTI images
by Antonella Kis 07 Oct '11

07 Oct '11

Dear FreeSurfers, I would like to know if there is a way to re-sample a NIFTI image (obtained after MRIcron conversion, from a dcm image) in Freesurfer with a scale factor of 2. I saw about mri_convert but this doesn't give me any option for the scale factor (for e.g. I want to drop each second slice from my NIFTI image) Thank you. AK

2 2

tracula -bedp - path
by Judit Haasz 07 Oct '11

07 Oct '11

Hi, I ran into 2 problems related to tracula. 1. trac-all -bedp command exits with following message. WARN: Running FSL's bedbost locally - this might take a while >> > WARN: It is recommended to run this step on a cluster >> > bedpostx_seychelles /usr/local/freesurfer/subjects/C001/dmri >> > subjectdir is /usr/local/freesurfer/subjects/C001/dmri >> > Making bedpostx directory structure >> > Queuing preprocessing stages >> > [: 223: NONE: unexpected operator >> > [: 314: NONE: unexpected operator >> > [: 327: xbedpostx_pre: unexpected operator >> > [: 486: x: unexpected operator >> > [: 486: -le: argument expected >> > Queuing parallel processing stage >> > [: 223: NONE: unexpected operator >> > [: 327: xbedpostx: unexpected operator >> > [: 486: x53: unexpected operator >> > 0 slices processed >> > Queuing post processing stage >> > [: 223: NONE: unexpected operator >> > [: 314: NONE: unexpected operator >> > [: 327: xbedpostx_post: unexpected operator >> > [: 486: x: unexpected operator >> > [: 486: -le: argument expected >> > This problem has been posted in May and June. bedpostx from command line runs perfectly and that is how I have been running it so far. One of u suggested to try the following: /usr/local/fsl/bin/bedpostx_single_slice.sh /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri 2 1 1000 1250 25 1 0 then I got: ** ERROR (nifti_image_read): failed to find header file for '/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000' ** ERROR: nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000): bad header info ERROR: failed to open file /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000 ERROR: Could not open image /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000 Image Exception : #22 :: Failed to read volume /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000 An exception has been thrown Failed to read volume /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/dmri/data_slice_0000Trace: read_volume4DROI. Done Can u suggest a reason behind all this? This happens on Linux machine (2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM Version: Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode). On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz 6-core Intel Xeon processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp runs well. My other question is: trac-all -path exists with error (in case of a single subject): Loading DWIs from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/dwi.nii.gz Loading mask from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri.bedpostX Loading segmentation map from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dlabel/mni/aparc+aseg.nii.gz Loading b-values from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/bvals Loading gradients from /disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/dmri/bvecs Segmentation fault Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Oct 7 10:21:20 CEST 2011 thanks for help. Judit

2 1

Inaccurate Surfaces Generated
by Jeff Sadino 07 Oct '11

07 Oct '11

Hi Freesurfer Team, When we tried to process some subjects in FS 5.0.0 through the cross-sectional step in the longitudinal processing stream, we got inaccurate surfaces generated. Also, after doing skullstripping or adding control points and re-running the cross-sectional reconstruction, inaccurate pial and white matter surfaces were generated (see attached pictures). We are not sure how to fix this problem and this has affected about 70 of our scans. Several of these subjects we also processed in FS 3 and FS 4.3.1, and the surfaces were generated fine. Are there any known solutions to fixing the surfaces in the newer FreeSurfer? If not, then could we feed the 4.3.1 cross-sectionals into FS 5 to create the base template, and then use FS 5 to create the longitudinal reconstructions? Thank you, Jeff Sadino

2 5

Freesurfer on Neurodebian
by Cartik Sharma 06 Oct '11

06 Oct '11

Hello there, Trying to work with cortical processing software Freesurfer for connectome related stuff. i've installed the s/w on NeuroDebian an debian virtual machine image. I'm getting some OpenGL warnings in running a command >tksurfer bert rh pial OpenGL Warning: vboxcall failed with vbox status code -8 OpenGL warning : SHCRGL_GUEST_FN_WRITE_READ (4543828) failed with *address* Seems like the CPU is still running and computation takes place at run time but results tend to take time to show up.. Is there a particular memory requirement for running Freesurfer on Neurodebian.. Thanks in advance. Cartik

1 0

nonconnexity and holes in parcels
by Ben Hamida Cammoun Leila Faiza 06 Oct '11

06 Oct '11

Hello, I am using freesurfer v5.1.0 (on ubuntu). when processing reconall on my data I notice on the parcellation aparc.annot two strange points: some isolated small regions not annotated, as well as the non connexity of some parcels. I checked the bert aparc.annot on inflated surface and I found the same problem of non connexity, for instance some medialorbitofrontal labeled vertices (vertex index 108562) in rostralanteriorcingulate, or vertex num 103429 labeled as insula in lateralorbitofrontal parcel. In lingual there is also a small hole without annotation like vertices: 35643,36746,37788..... is this normal? if yes, how can we correct that? thanks in advance

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Freesurfer October 2011