Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

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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Matlabpool has been removed
by Kasper Jessen 23 Mar '16

23 Mar '16

Dear FreeSurfer experts, Thanks again for a great FreeSurfer forum. I have been trying to run the linear mixed effects model on a longitudinal dataset. However, i get the an error in matlab: "matlabpool has been removed. Use PARPOOL instead". I can see in the forum that others have experienced the same. Unfortunately i cannot find the answer, which fixes the problem. As far as i understand, it may be because i am using a new version of Matlab. However, is there a way to fix the problem? Best regards, Kasper Jessen MD, PhD student

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mris_anatomical_stats on more than one subject at a time?
by Elissa Ash 22 Mar '16

22 Mar '16

Dear experts, Is there any way to run the mris_anatomical_stats command on more than one subject at a time? Thanks, Elissa -- Elissa Ash, MD, PhD Director, Center for Memory and Attention Disorders Department of Neurology Tel Aviv Sourasky Medical Center 6 Weizmann St. Tel Aviv 64239, Israel 972-3-6973698 fax: 972-3-695-0365

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mris_flatten error
by Ji Won Bang 22 Mar '16

22 Mar '16

Dear. Freesurfer experts. Hi. How are you? I'm trying to flatten the visual cortex using the command mris_flatten (freesurfer version 5.3.0). The command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat The error I get is: using write iterations = 0 sampling 7 neighbors out to a distance of 12 mm reading patch /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with 27964 vertices (19.0% of total) MRISreadPatch: bad vertex # (147220) found in patch file No such file or directory Previously, Bruce advised me to recut it, so I deleted the lh.oc.patch.3d and recut it. However, freesurfer gives me the same error message... Could you please help me fix it? Thank you so much. Best, Ji Won

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PET voxelwise
by Elijah Mak 22 Mar '16

22 Mar '16

Hi Freesurfer Community, I am trying to run a vertex-wise analyses of PET data. I have already performed bbregister. Next, I did mri_vol2surf for each subject, left and right hemispheres. for i in `cat subjects`; do mri_vol2surf --src FS6_${i}_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out FS6_${i}_MPRAGE_Neuro.nii/surf/lh.PETSurface.mgh --hemi lh --regheader FS6_${i}_MPRAGE_Neuro.nii --projfrac 0.5 --interp nearest; done Is this command correct? Visual inspection on freeview looks OK. How may I derive the group average from these individual surfaces and perform the mri_glmfit? Any help will be greatly appreciated. Best Wishes, Eli

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