Freesurfer June 2014

freesurfer@nmr.mgh.harvard.edu

155 participants
234 discussions

recon-all CUDA error
by Chiu, Bryan (PHTH) 27 Jun '14

27 Jun '14

Hi, I'm fairly novice at Linux and I've been trying to setup CUDA for recon-all. I get an error as follows: [TLA@COGMOB-linuxPC ~]$ recon-all -s bert -use-gpu -openmp 8 Testing for CUDA device: /usr/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux COGMOB-linuxPC 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Fri Jun 27 10:53:29 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any idea what is going on? I setup CUDA and my Nvidia drivers according to this tutorial (http://aspratyush.wordpress.com/2012/05/06/install-nvidia-cuda-on-centos-6/) With, of course some slight changes to install the latest toolkit. Thanks in advance, - Bryan

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Vertex-wise comparison thickness left and right hemisphere
by Martijn Steenwijk 27 Jun '14

27 Jun '14

Dear all, I would like to vertex-wise compare the left and right hemisphere thickness in a group of subjects. Would it be okay to just substract lh.hickness.0.mgh and rh.thickness.0.mgh (i.e. the files concatenating the thicknesses of all patients), then smooth and then perform a one sample t test? Or does freesurfer include a more sophisticated test to perform such a comparison? Best, Martijn

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Re: [Freesurfer] Question about eTIV estimation
by Zia, Mohammad 26 Jun '14

26 Jun '14

Hi, Thanks for the replies and link. And sorry for the double post. Thanks, --Mohammad This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original.

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Question about eTIV estimation
by Zia, Mohammad 26 Jun '14

26 Jun '14

Hi, Does the eTIV estimate include the CSF between the dura mater and pia mater? Thanks, --Mohammad This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original.

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Question about eTIV estimation
by Zia, Mohammad 26 Jun '14

26 Jun '14

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How to use clusterwise correction for multiple comparisons in Freesurfer
by Miao Wei 26 Jun '14

26 Jun '14

Dear Freesurfer experts, My dataset was processed by Brainsuite, so that after registration they are in .dfs format. Now I wanted to do multiple comparison correction. How do I import the data to freesurfer and do the corrections? Thanks. Miao

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Longitudinal preprocessing troubleshooting
by Chiu, Bryan (PHTH) 26 Jun '14

26 Jun '14

Hi all, I have a set of data with ~75 subjects with up to 4 timepoints of scans. The structure of the data indicates that it would be best processed using a longitudinal design. I have recon-all most of the scans. There are a few scans that I am worried about and wondering how to treat each case. I do one sanity check with freeview using a modified version of bert's command: "freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red" 1a) Skull strip or underanalysis errors: I have attached one screenshot of a very severe case of an underanalysis. How should I treat this case? I have recently read about Editing a Recon in Freeview, but I'm not sure how to proceed with this. b) Skull strip errors -- Some scans have a very small amount of cerebral cortex labelling into the dura mater/ skull. Does this warrant the manual removal via freeview of the skull? 2) Since I am running this through the longitudinal processing, could I be able to skip #1 hoping that the averaging of the timepoints into a 'base' will remove these issues? 3) I have 2 brains that are completely whited out in Freeview (see attached). However the analysis went through and it looks good to me. Opening the raw Nifti file in mricroGL does not show this at all. What is going on and should I be concerned? 4) I have 2 other brains that failed the recon-all. One of them is a Talairach fail and the other one failed mri_watershed. Looking at these brains in mricroGL shows a dark shadow being cast over the brain running diagonally from the front of the head to the back. I think this is the root of the problem. Is there a way to fix this or should I consider these scans problematic and exclude them? Regards, - Bryan

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Re: [Freesurfer] Correcting left-right flip for multiple subjects at the same timepoint
by Chiu, Bryan (PHTH) 26 Jun '14

26 Jun '14

The output brain is that which I see from freeview. I usually check their sulci and gyri to confirm if a scan is good. I resolved the issue by rerunning my PAR/REC files through the same dicom to nifiti converter for all of them. It turns out the person before me used a different tool which resulted in incongruent scans of the same participant through multiple timepoints. Thanks, - Bryan

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Qdec Annotation to Individual
by Tara Ann Miskovich 26 Jun '14

26 Jun '14

Hello, I was hoping someone could help me map with mapping my annotation from my significant qdec clusters into each individual space. Thanks! Tara Tara A. Miskovich, B.A. Affective Neuroscience Laboratory Department of Psychology University of Wisconsin-Milwaukee 334 Garland Hall miskovi2(a)uwm.edu

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mri_segstats question
by Martins, Brad 26 Jun '14

26 Jun '14

Hi everyone, I’m new to Freesurfer and I have a question about the output of mri_segstats. I have created an ROI in which I am measuring cortical thickness. When I run mri_segstats I get a table with 2 rows of segmentation values. What are the 2 rows? The SegId of the two rows are 0 and 1 but I don’t know what segmentations that corresponds to or where to find out. Any help would be greatly appreciated! Thanks, Brad

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Freesurfer June 2014