Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

mris_make_surfaces in longitudinal stream - explanation of parameters
by Antonin Skoch 18 Nov '16

18 Nov '16

Dear experts, I am trying to understand how the pial and white surfaces are generated in longitudinal stream using information from the reconstructed base template (freeSurfer development version). In longitudinal stream, apart from the -orig, -orig_pial and -orig_white there are also parameters -long and -max 3.5. May I ask what is the significance of these parameters? -max 3.5 means constraining cortical thickness to 3.5 mm? Why this constraint is applied specifically in longitudinal stream? In mris_make_surfaces.c I found that -long means that initial pial vertex positions are set between final white and orig pial, slightly inside orig_pial. What is the significance of this setting in longitudinal stream? Last question, not related specifically to longitudinal stream: What is the difference between -orig and -orig_white parameters of mris_make_surfaces? From the reading of source codes (quite tough to me) I got an impression that from -orig the gray and white matter histogram values are computed whereas -orig_white defines initial position of the vertices in the first iteration (which, for some reasons, does not necessary has to be identical to -orig). Am I correct? Regards, Antonin Skoch

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Re: [Freesurfer] Questions about outputs in Longitudinal Stream
by Tamara Tavares 18 Nov '16

18 Nov '16

Thank you for the clarification Martin I have a follow-up question. When I load the base to make sure it doesn't look blurry, should I check the norm.mgz or brainmask.mgz? Online says norm.mgz but I just want to make sure. Also, would the "blurriness" be obvious? Similarly, when I open the base and the longitudinal runs to see whether they align, again should I load the brainmask.mgz for these as well? Thank you in advance for your help, Tamara

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Re: [Freesurfer] Two Stage Longitudinal Model
by Timothy Hendrickson 18 Nov '16

18 Nov '16

Hi Martin, Thank you for your reply. I am glad to hear that I am doing that correctly. I am running into an error when I attempted to run my GLM. I have looked at my fsgd and qdec files for errors, however I cannot seem to find anything. The error is in the attached .txt file named illCondMatrix_twoStage_years_10_31_16.txt. Additionally I've included my fsgd file for stage two and my qdec file for stage one. Any assistance would be extremely helpful, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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Longitudinal analysis
by Jaiashre Sridhar 18 Nov '16

18 Nov '16

Hi FreeSurfer Team, We are doing a longitudinal analysis with three time points which are six months apart. The subjects at any time point were scanned on either one of the two scanners (both Siemens 3T TIM TRIO) and we used FreeSurfer v5.1 for our analysis. Most of the subjects show decrease in cortical volume over time except a few of them, who show a huge increase in volume at their 6th-month visit (or at their 12th-month in a couple of cases). When we tried to look at the reconstructed surfaces of the long brains in Freeview, the gray matter and white matter boundaries of the 6th-month were bigger overall than the boundaries of the baseline and 12th-month. Could you share with us your thoughts on what factors (with MPRAGE/Scanner/FreeSurfer) might have caused this problem? Thank you, Jaiashre.

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What is the latest 'supported' CUDA version?
by June Kang 17 Nov '16

17 Nov '16

Dear freesurfer developers, Anybody know which CUDAversion is the latest one supported by freesurfer? I just found the thread below. it's written in 2014, but experiences same error.Successful detectcuda command, but core dump during very first step of recon-all. https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36769.html Now I am trying to remove CUDA 8 and installing CUDA 5.5. Next will be the CUDA5.0If anybody knows what is the 'supported' or 'successful' late cuda version, please let me know.Bests,

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load_analyze_hdr.m: incomplete hdr struct with modified hdr.hist.originator field
by Kathryn I. Alpert 17 Nov '16

17 Nov '16

Dear FS developers, Firstly, let me thank you for FreeSurfer: I use FS almost daily, and it is fantastic. Now, onto the bug report: When reading an analyze header with a modified hdr.hist.originator field, load_analyze_hdr.m sometimes “runs out” of bytes and leaves the last field (hdr.hist.smin) empty. When I pass the hdr struct to write_analyze_hdr.m, an invalid, 344 byte header is written (due to this empty hdr.hist.smin field). I will explain how to replicate the issue after first explaining what I think is happening and how I think it can be fixed. I notice that on line 119 of load_analyze_hdr.m, the comment reads “Is this correct? Should be unsigned char”; so, perhaps someone had this issue previously, or hand an inkling that the code was problematic. Because of varying character encodings, fscanf(fp,’%c’,10) may read more than 10 bytes, which means all later fields will not be set properly. The fix is simple, and there are a few options: 1) When opening the hdr file, force ‘US-ASCII’ encoding so each character is precisely 1 byte: (lines 59 and 63) fp = fopen(hdrfile,’r’,’b’,’US-ASCII’); (line 75) fp = fopen(hdrfile,’r’,’l’,’US-ASCII’); *This is the preferred solution as it preserves the “readability” of the field. It also would apply to all the other instances of fscanf.* 2) use fread with uchar (line 119) hdr.hist.originator = fread(fp,10,’uchar’); 3) use fread with char*1 (line 119) hdr.hist.originator = fread(fp,10,’char*1’); I noticed this bug in the following context. I received a nifti file with an incorrect resolution in the header. When I corrected the resolution using matlab (load_nifti.m -> correct nii.pixdim -> save_nifti.m), converted the nifti image to analyze (mri_convert -ot analyze in.nii out.img), loaded the resulting analyze header in matlab with hdr = load_analyze_hdr(‘out.hdr’), and tried to run write_analyze_hdr(hdr,’new.hdr’), the new.hdr file was an invalid, 344 byte header file. I would be happy to send along sample images if needed. I am hoping that you will add this fix to later versions of FreeSurfer, and perhaps consider updating 5.3.0, as well. Thanks and best wishes, Kate *Kathryn I. Alpert* Software Developer, Neuroimaging and Applied Computational Anatomy Lab Northwestern University Feinberg School of Medicine 312.725.2832 k-alpert(a)northwestern.edu [image: Feinberg School of Medicine] *Educate, Discover, Improve Health*

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CUDA problem in ubuntu with M4000 card.
by June Kang 17 Nov '16

17 Nov '16

Dear Freesurfer + CUDA users, I am trying to run cuda-enabled recon-all procedure.My system is Ubuntu 14.04, NVIDIA M4000, with freesurfer stable beta 20161028 + CUDA 8.0 driver. I get the error message like below. $ recon-all -all -s DEP030 -use-gpu Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221Driver : 8.0 Runtime : 8.0Acquiring CUDA device Using default device CUDA device: Quadro M4000 Segmentation fault (core dumped) Linux DTI 3.13.0-101-generic #148-Ubuntu SMP Thu Oct 20 22:08:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s DEP030 exited with ERRORS at 2016. 11. 18. (금) 07:54:00 KSTFor more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting the detectcuda command seems can get M4000 properly.Detecting CUDA... There are 0 devices supporting CUDA:Device 0: "Quadro M4000" CUDA Driver Version: 8.0 CUDA Runtime Version: 8.0 CUDA Capability Major revision number: 5 CUDA Capability Minor revision number: 2 Total amount of global memory: 4219863040 bytes Number of multiprocessors: 13 Number of cores: 572 Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total number of registers available per block: 65536 Warp size: 32 Maximum number of threads per block: 1024 Maximum sizes of each dimension of a block: 1024 x 1024 x 64 Maximum sizes of each dimension of a grid: 2147483647 x 65535 x 65535 Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Clock rate: 0.77 GHz Concurrent copy and execution: Yes Run time limit on kernels: Yes Integrated: No Support host page-locked memory mapping: Yes Compute mode: Default (multiple host threads can use this device simultaneously)

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Problem with wm/pial surfaces
by Sneha Pandya 17 Nov '16

17 Nov '16

Hi team, I am having problem with almost all the subjects in which wm/pial surfaces are not estimated correctly. These subjects are suffering from Corticobasal degeneration or progressive supranuclear palsy. I tried running sample of these subjects with multiple T1s as input (as we had them) and with additional parameters: -FLAIR, -FLAIRpial, -norm2-b 20, -norm2-n 5, -3T, and -bigventricles. These are either mprage or spgr sequences with 1x1x1 resolution. Flair input did not help instead made pial surfaces worst and convoluted (blue) as opposed to *.woFLAIR.pial surfaces (magenta), and even with addition of other flags it did not further improve estimation of wm/pial surfaces as seen in attached screenshots. The only option being adding control points. But these are about 200+ subjects, and I am not sure if to trust the manual edits on such a big scale. Can anyone please suggest any other tweaks I could try? [cid:01f72aae-1e98-4f12-bcf1-d2e3639dc992] [cid:d1acff28-76d5-4cbf-aa2b-8fb55a07abfe] Thanks, Sneha

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creating label that is the overlap between two other labels
by Harry R. Smolker 17 Nov '16

17 Nov '16

Hello, I have two labels (generated from qdec analyses) that have some overlapping vertices. I am interested in creating a label that is just the overlap of the two aforementioned labels. Is there a way to do this using Free Surfer tools? Thanks, Harry Smolker

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Problem using mri_cor2label
by Sophie Wohltjen 17 Nov '16

17 Nov '16

Hi, I am trying to create cortical surface labels from several brain masks. All are .mgz files, separated by hemisphere, and aligned to fsaverage. Here is the command I entered to create the labels: mri_cor2label --i <filename>.mgz --l <labelname>.label --id 1 When I run this command, I successfully create the label, but I am unable to open the label in tksurfer. I've tried opening both from the GUI menu and from command line, and each time I get the following error: -- ******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 13245 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... MatrixMultiply: m2 is null! -- And then tksurfer closes. I'm not sure why this is happening -- any help would be greatly appreciated! Thanks, Sophie

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Freesurfer November 2016