Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

ventral DC
by Yang, Daniel 31 May '13

31 May '13

Dear all, in the aseg.volume, there is a term called 'ventral DC' and I am wondering what it is. I looked up the previous posts and know DC = diencephalon, and it's a grab bag of stuff that cannot be resolved. However, does anyone know what exactly ventral DC is? Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

2 2

Freeview automation
by Garikoitz Lerma-Usabiaga 31 May '13

31 May '13

Hi list, is it possible to automate Freeview automation from the command line? I want to automatically render 3D images of the hippocampus (I have a separate volume, based on hippo-subfields) and have an image for all subjects for quality checking. thanks! Gari

4 7

Importance of Segmentation/Parcellation edits with respect to cortical thickness
by Jonathan Holt 31 May '13

31 May '13

Hi all, We are using the parcellation of Desikan-Killiany https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation and creating labels for each structure in each hemisphere with: mri_annotation2label --subject ${SUBJ} --hemi ${HEMI} --outdir ${SUBJ}/${SUBJ}_annotate and making matlab text readable (via matlab load command) thickness files with: mris_convert -c ${HEMI}.thickkness ${HEMI}.white ${HEMI}.thickness.asc Then we are reading in the ascii thickness files and the labels and creating histograms (unit area) for each structure for each participant, essentially following: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIma keahistogramofcorticalthickness.3F We've dropped the zeros but also dropping values of thickness identically = 5mm. The question is: How important are parcellation edits, that is how accurate are the generated segmentation labels, and should we be dedicating effort to ensuring they're accurate and possibly editing them if not (if so, what should be used as a guide/template?) jon

2 1

Average for each voxel across all conditions
by Katie Bettencourt 31 May '13

31 May '13

Hi, I have an experiment where I have 3 conditions in a FIR event related analysis (running FS 4.5). I need to get the mean activity level for each voxel across all conditions across the run, so that I can calculate percent signal change for each individual voxel. Is this available (I have analyzed each run separately) somewhere? Katie

2 2

recon-all errors: v5.0.0; dataset 4
by Sudhin A. Shah 31 May '13

31 May '13

CORRECTING DEFECT 1 (vertices=33, convex hull=57) After retessellation of defect 1, euler #=-41 (88676,260208,171491) : difference with theory (-61) = -20 CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s IN387G exited with ERRORS at Thu May 16 05:11:49 EDT 2013

2 2

Editing after reconstruction
by Cristian Paz 31 May '13

31 May '13

Hello FS-ers, I have a beginner question. I am wondering about editing. Since I have no superior of me in my lab to inspect or guide me in my freesurfer analyses - I get a bit worried that I might oversee some important errors from recon-all. If there is nothing that is strikingly wrong in the output from recon-all - should I then expect my results to be good enough for group analyses? If there is no error messages, and nothing that looks strange when I open rsults in tkmedit (for a beginner)? How often does a reconstruction from Freesurfer need to be edited,(roughfly, on average) if you have a group of lets say 32 subjects ? thank you so much for your help! best regards, Cris

2 1

Correction for multiple comparisons error
by Fotiadis, Panagiotis 31 May '13

31 May '13

Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x0000000006e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x0000000006e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos

3 14

TRACULA outputs out of expected range
by Ali Ezzati 31 May '13

31 May '13

Hello Experts, I would be grateful if you could help me with this problem: I was able to run all steps of TRACULA on several subjects without any error message, but all the final outcomes (FA,MD,RD,AD values) are out of the expected range (i.e average FA values for all tracts are >1). I tried to identify the source of this problem... clearly FA values in "dmri/dtifit_FA", which is an output of "prep" step are all out of range. The only source of error that I can think of is .bvecs file. My input .bvecs files are in 3 columns, exactly as described in the manual. There are two .bvecs file in the "dmri" folder. one is "dwi_orig.mghdti.bvecs" which is exactly the same as my input .bvecs file and the other one's name is just "bvecs", which has completely different values. Could this be the source of my problem? or something else is causing this. Thank you, Ali

2 5

CUDA install; libcudart; 64-bit detection
by Graham Wideman 30 May '13

30 May '13

Hi all, probably mostly Bruce and co., I've just got a new linux box set up and am able to run all graphical tools and recon-all OK. Linux Mint 15 x64 RC (based on Ubuntu 13) Intel i5 Ivy Bridge nVidia GTX 650 Ti nVidia drivers: Selected from System > Device Drivers; nvidia-313-updates; automatically installed. Freesurfer 5.3 Centos 6 version Now I'm hoping to get CUDA working. The proximate problem is that when I run Freesurfer's cudadetect I get: "error while loading shared libraries: libcudart.so.5: cannot open shared object file: No such file or directory" Indeed, searching the file system, there appears to be no libcudart.* anywhere. But there do appear to be CUDA components installed with the installation of the nvidia video driver: /usr/lib/nvidia-313-updates/libcuda.so 10.4 MB (plus some version-named links to same) So, my current model is that nvidia has installed what it considers to be the necessary components for an application to use to operate the CUDA hardware. Googling around, there seem to be some mentions that libcudart.so.* is something that would be supplied with a particular application (in this case Freesurfer). I'm not sure I believe that, but... The only other alternative I see is to download the nvidia CUDA developer kit and install that. However I'm very loath to do that because it replaces the video driver along with installing a lot of other unneeded apparatus. I have no idea the extent to which that installation works with or against the Ubuntu/Mint installation scheme, and what would happen on next video driver update. Not to mention that the latest Ubuntu-compatible package nvidia has is for 11.10, while my Mint is based on Ubuntu 13. Any idea how to proceed? Any chance of getting libcudart.so.5 a la carte? SIDE NOTE ON 64-bit detection in cuda_setup ============================================ I see that in script cuda_setup there's a section which detects 64-bit by looking for directory: /usr/lib64 However, on Mint (so I assume Ubuntu and Debian) 64-bit, there is no such directory. Instead, there are: /usr/lib /usr/lib32 Suggestions for other ways to detect 64-bit: http://stackoverflow.com/questions/246007/how-to-determine-whether-a-given-… I'm pretty sure this is not pertinent to the hunt for missing libcudart.so, but seems like that needs to be fixed too for Ubuntu/Mint. ---------------- Thanks, -- Graham

1 0

recon-all error
by Borzello, Mia 30 May '13

30 May '13

Hi freesurfers, I encountered an error using recon-all for a scan series of 177 slices. I'm not sure exactly why it errorred, but I included the error log. Thanks so much, Mia

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