Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

errors message in QAtools
by Lars M. Rimol 24 Mar '16

24 Mar '16

Hi, I'm running QAtools on a set of subjects processed with FS 5.3.0, and consistently get this message when recon_checker is running: Processing each subcortical label ... (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error etc. *And in the recon_check file I notice several of my subjects have this error message:* ERROR: Recon-all steps missing in subject <SUBJ_ID> status file Expected to see the following step(s): #@# Remove Neck ti. 22. mars 15:02:33 +0100 2016 in the recon-all-status.log file before (line # 12): --> CA Reg Inv *I ran recon-all -all, and the recon-all log file seems to indicate neck removal was peformed*; from recon-all.log: mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... -- writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 51 seconds. #-------------------------------------- #@# SkullLTA ti. 22. mars 14:45:17 +0100 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 -- reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... Apart from this, the snapshots look ok (except for one subject I asked about in a previous e-mail) and there are no outliers in any of the subjects (according to QAtools). Any idea why I get this error message? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital 7006 Trondheim, Norway

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OpenMP and GPU implementation in freesurfer 6 beta
by Francis Tyson Thomas 24 Mar '16

24 Mar '16

Hi, I have been working on speeding up the the hippocampal segmentation in freesurfer 6 beta and I have been playing around with both -openmp and -use-gpu flags. I noticed that freesurfer does seem to make use of all the threads in freesurfer 6 irrespective of passing the -openmp flag or not. Is that the right behaviour. I found this by analysing the cpu usage in both the cases. Also, it looks like development for GPU usage has been halted for now and so I was trying to use the CUDA 5 for getting it working under ubuntu 14.04. I have been not successful that as the cuda device isn't getting selected. Do you have any recommendations on that? And lastly, there is the itkthreads option available to -hippocampal-subfields-T1, so can I combine all three or two of these options to minimize the execution time - like GPU and itkthreads or GPU, OPENMP and itkthreads? Also the v6 beta is no longer available on your website. Is there any particular reason as to why it was removed and can I continue using the copy that I have for hippocampal segmentation ? Thanks, Tyson

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Surface based analysis using FA maps
by Alshikho, Mohamad J. 24 Mar '16

24 Mar '16

Dear FS experts, I would like to run surface based analysis using FA maps. I am not exactly sure that what I am doing is totally right specially step 2 . I used the following commands: 1. I registered the FA maps to T1 using the command: bbregister --s bert --mov dtifit_FA.nii --bold --init-fsl --reg reg.dat 2. I concatenated the subject's FA maps using the command : mris_preproc -target fsaverage -hemi lh -iv .bert1/dtifit_FA.nii reg.dat -iv bert2/dtifit_FA.nii reg.dat .... --projfrac 0.5 --out lh.FA.mgz 3. Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.FA.mgz --tval lh.FA_5mm.mgz 4. Then GLM analysis using mri_glmfit 5. Correction for multiple comparison mri_glmfit-sim Kindly, are these steps correct? I used the previous steps to do surface based analysis using PET images and it worked very well. While for the FA maps it seems that there is something wrong and I can't figure out what it is! I highly appreciate any input on this! Best, Mohamad

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recon-all exited without error, but localGI crashed
by Lars M. Rimol 24 Mar '16

24 Mar '16

Hi, I'm running recon-all on a cluster using Linux, 64 bit Centos 6. Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. I first run recon-all -all, then recon-all -localGI One out of 102 subjects failed the lgi, but the recon-all -all excited without error. During "Computing MAP estimate", however, it did give this error (multiple times): IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA But I find that in several subjects who also exit recon-all -all without error, so I assume that's OK? When it exited recon-all -localGI, it produced this warning: ... remeasuring lGI value for vertex iV = 73001. It may take a few minutes. WARNING -- Problem for vertex iV = 73001, lGI value is aberrantly high (lGI=48.6608)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/usit/abel/u1/rimol/subjects/PD/PD008/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'! Linux compute-16-31.local 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Although recon-all -all exited without error, should I still be worried, since it appears that there may be topological defects in the pial surface? I've looked at the surfaces and there is one spot that looks suspicious (please see attached screen shot from Freeview). Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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mri_label2vol check-up
by Ji Won Bang 23 Mar '16

23 Mar '16

Dear. Freesurfer experts. Hi. How are you? I'd appreciate it a lot if you can help me with this problem. I'm trying to check the ROI (.nii) after creating it by using mri_label2vol command. I used the command: mri_label2vol --label $SUBJECTS_DIR/$SUBJECT/label/lh.v1vt.label --label $SUBJECTS_DIR/$SUBJECT/label/lh.v1dt.label --temp $DATA_DIR/$SUBJECT/bold_retino/025/fmcpr.nii.gz --reg $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat --o $DATA_DIR/$SUBJECT/roimask/test.nii tkmedit -f $SUBJECTS_DIR/$SUBJECT/mri/norm.mgz -overlay $DATA_DIR/$SUBJECT/roimask/test.nii -overlay-reg $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat -fthresh 0.01 However, this tkmedit command looks for test.dat file instead of test.nii and does not show ROI. Could you please tell me what's going wrong? Thank you! Best, Ji Won

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XNAT Freesurfer custom datatype
by Rockers, Elijah D. 23 Mar '16

23 Mar '16

Trying to integrate freesurfer data with our XNAT database. Are there any freesurfer schemas for XNAT available, or is it pretty much I have to try to make my own? Thanks, -- Elijah Rockers Research Data Analyst Houston Methodist Neurological Institute O: 713 363 7729 Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties and designated as a Magnet hospital for excellence in nursing. Houston Methodist has also been named to FORTUNE® Magazine's "100 Best Companies to Work For®" list for 10 years in a row. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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cannot allocate memory
by Ehsan Tadayon 23 Mar '16

23 Mar '16

Dear Freesurfer experts, I'm trying to run mri_vol2vol on a functional mri to resample it onto orig.mgz. I get this error: ``` mri_vol2vol(98217,0xa0ce01d4) malloc: *** mach_vm_map(size=262144) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13664th slice Cannot allocate memory ``` I was wondering if you have any suggestions. Thanks in advance for your time. Best, Ehsan.

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Re: [Freesurfer] PET voxelwise
by Elijah Mak 23 Mar '16

23 Mar '16

Hi Doug, Thanks! I manually tweaked the registration of the PET to T1 on a number of subjects to bring the mincost down to < 0.5. After saving the pet2free volume in Freeview, I noticed that a new .lta is produced in the same directory (i.e. pet2free_fsl.mgz.lta). Will the option --regheader tell the subsequent commands (i.e. mri_vol2surf) to use the updated registration .lta instead of the original .dat that was produced via bbregister? Best Wishes, Elijah

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Re: [Freesurfer] PET voxelwise
by Elijah Mak 23 Mar '16

23 Mar '16

mri_concat --f pib_lh_fsaverage (textfile of subjects and their images) --o concat_lh_pet.mgh Should I add -mean here for the GLM? mri_glmfit --y concat_lh_pet.mgh --fsgd pib_fsgd --C group1.group2.mtx --surf fsaverage lh --cortex --glmdir lh.pet.glmdir My simple 2 group-no-covariates FSGD is as follows. Can I also check that it is alright to have the Groups interspersed throughout the order? GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 input FS6_16084_MPRAGE_Neuro.nii Group1 input FS6_22769_MPRAGE_Neuro.nii Group1 input FS6_22863_MPRAGE_Neuro.nii Group1 input FS6_22899_MPRAGE_Neuro.nii Group1 input FS6_22995_MPRAGE_Neuro.nii Group2 input FS6_23008_MPRAGE_Neuro.nii Group1 input FS6_23173_MPRAGE_Neuro.nii Group2 input FS6_23243_MPRAGE_Neuro.nii Group2 input FS6_23244_MPRAGE_Neuro.nii Group1 input FS6_23619_MPRAGE_Neuro.nii Group1 input FS6_23623_MPRAGE_Neuro.nii Group1 input FS6_23755_MPRAGE_Neuro.nii Group2 Thanks again, Doug. Appreciate it so much! Best Wishes, Elijah

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Troubleshooting for error - neither NIfTI-1 qform or sform are valid
by Reema Jayakar 23 Mar '16

23 Mar '16

Hi Dr. Greve, Thank you very much for getting back to me so promptly. If memory serves me right, I am pretty sure that the orientations were incorrect in tkmedit but will double check soon. Based on what you are saying and based on what I read in the wiki about mri_convert it seems that I will be able to change all of my nifti files using mri_convert and then I can use the newly generated niftis to run reconall? Is this correct? As I am very new to FS, I don't know what it means to give it an orientation string? Is there some documentation where I can look this up further? In any case, thank you very much and I will keep you posted! Best, Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayakar1(a)student.gsu.edu Message: 24 > Date: Tue, 22 Mar 2016 10:56:40 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1 > qform or sform are valid > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <56F15D28.7040207(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > To check whether the orientation is correct, you can view it in freeview > or tkmedit. When you click on the axial view it should show up axially, > etc. Though you cannot tell whether it is left-right reversed this way. > You cannot feed it a matrix, but you can specify the direction cosines > on the mri_convert command line (-iid, -ijd, -ikd). You'll have to play > with it a bit. You can also try giving it an orientation string instead. > if you run mri_convert without any options, then it will give you lots > of documentation. > > On 3/20/16 8:44 PM, Reema Jayakar wrote: > > Hello FS list subscribers, > > > > Is there a way to manually feed FS with NIfTI-1 qform or sform > > information? Or correctly add this information to the original .nii > > files? My sense of the problem is that there is a problem with the > > header information in my .nii files and FS cannot tell what is > > anterior, posterior, left, right. > > > > That said, I am very new to FS and my interpretation of the error > > could be wrong. So I am laying out the details below (recon-all.log is > > also attached to this email): > > > > * When I try to run recon-all there are no output images/files > > generated and the message I get is that the Talairach transform > > failed > > * When I try to run autorecon1 an autorecon2 with the "-notal check" > > flag, FS does not give me any error message and proceeds with > > generating output. However, I can visually see (via brainmask.mgz) > > that oreintations are messed up (e.g., tried to register coronal > > orientation on top of sagittal orientation) > > * This problem only occurs with .nii files from a particular study > > that came out of a specific scanner. All my other data are running > > through FS smoothly, which is why I think there is some problem > > with the .nii files > > * Also, when I view my raw .nii images in FSL view none of the usual > > orientation markers are visible to me, which again suggest that > > they may be missing? > > * Unfortunately, I do not currently have the original .dcm files > > available as this is a multi-site archival study > > > > > > Any help you can provide to resolve this issue would be really > > appreciated! > > > > Thank you, > > Reema > > > > > > > > -- > > *Reema Jayakar, M.A.* > > Doctoral Candidate - Clinical Neuropsychology > > Health Resources and Services Administration (HRSA) Fellow > > Department of Psychology > > Georgia State University > > Email: rjayakar1(a)student.gsu.edu <mailto:rjayakar1@student.gsu.edu> > ******************************************* >

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Freesurfer March 2016