Freesurfer March 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
172 discussions

Matlab error in Freesurfer
by Miguel Ángel Rivas Fernández 14 Mar '19

14 Mar '19

External Email - Use Caution Dear Freesurfer experts, I am trying to run Freesurfer commands (eg. mri_ca_label) using Matlab in a Mac computer (macOS High Sierra 10.13.6 version) and I'm receiving the following error that I suspect are due to library incompatibilities: dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib mris_ca_label -aseg /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234 10018 lh /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Aborted ans = 134 I realized that this error has been previously reported <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054961.…> and, as Andrew said, one of the possible solutions could be to disable the SIP (System Protection Integrity). I have disabled the SIP following the instructions indicated here <http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection…> but unfortunately Matlab continues giving the same error. How could I solve this problem?. Any help would be appreciated. Thanks in advance. Best, -- *Miguel Ángel Rivas Fernández*

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Model the FS-FAST pre-processed data with SPM
by Zhi Li 14 Mar '19

14 Mar '19

External Email - Use Caution Hello Freesurfer experts, May I know if it is possible to transform the FS-FAST pre-processed data (left surface + right surface + subcortical region) to SPM-readable format? How could I combine the three pre-processed data together and transform them back to volume-based dataset? I would like to get the confounds matrix (filtering + whitening) during model specification and estimation that I could not find in FSFAST. Hence I want to model the FS-FAST pre-processed data with SPM. Any suggestions? Many thanks and best regards, LIzhi

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Segmentation fault
by Donatienne Van Weehaeghe 14 Mar '19

14 Mar '19

External Email - Use Caution Dear, I encountered the following error when I tried to run mri_gtmpvc -- rbv: Segmentation fault (core dumped) First I performed the PET to orig registration using spmregister, secondly I tried with the registration using mri_coreg but the error remained. I also redid the segmentation step gtmseg --s $word --xcerseg without fixing the problem. Can anyone help me with this problem? The code I tried to run: #mri_gtmpvc --i SUVR_cerebellum.nii.gz --reg suv.reg.lta --psf 5 --seg /gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o gtmpvc.output.suvrcerebellum.spmreg --no-rescale --threads 8 Kind regards Donatienne

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LGI in QDEC
by 郑凤莲 14 Mar '19

14 Mar '19

External Email - Use Caution Hi experts, I am using qdec software for the statistic of LGI. I have created the .Qdecrc file. However, when I set Monte Carlo Null-Z Simulation (fwhm=10), there is an error: "Error running mri_surfcluster, Error: fwhm out-of-range(<1 or >30)". Then, I set fwhm at 5, it is ok. By the way, there is no error in the statistic of cortical thickness, surface area and volume, just in LGI. Is there any way to solve this problem？Or how can I describe this difference on fwhm? I really need your help. Look forward to your reply. Thanks! Sincerely, Zheng

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dt_recon multiple dti scans
by Daniel Callow 14 Mar '19

14 Mar '19

External Email - Use Caution Hello Doug, If I collected 3 dti scans at each time point and I wanted to know how would I go about incorporating them all into dt_recon to improve my SNR? Could I just pull all the DICOMS into 1 folder? Or process each one separately? Thanks, Daniel -- *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Errors when visually inspecting aseg.mgz
by Maria-Eleni Dounavi 14 Mar '19

14 Mar '19

External Email - Use Caution Dear Freesurfer developers and users, I am running the freesurfer recon-all pipeline for a big dataset and I am particularly interested in the hippocampus. For 20% of my subjects the hippocampus along with other subcortical structures are misplaced in the aseg.mgz image, which affects also the subsequent subfield analysis. ? I was wondering which steps must be followed to fix this and which surfaces need to be corrected. So far I have corrected/checked the initial brain mask and added control points to the analysis but there is no difference in the end result. I would be grateful if you could let me know how to tackle this issue. Apologies if a similar question has been asked in the past and I missed it. Best Wishes, Marialena

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recon-all to fsaverage
by Laboratorio de Neurociencia Funcional 14 Mar '19

14 Mar '19

External Email - Use Caution Dear Freesurfers, I would like to apply recon-all to the fsaverage subject of my sample to get all the labels that are obtained in each individual subject. However, it is not possible because my average subject doesn't contain the file /orig/001.mgz required to run the recon-all. Could you help me to handle this issue? Many thanks in advance. Best regards, Jose

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ROI mask extraction from asec and apark
by Tim Hahn 14 Mar '19

14 Mar '19

External Email - Use Caution Dear Freesurfer experts, as far as I understand, Freesurfer employs the Desikan-Killiany Atlas (by default) to compute the various parameters based on the aseg and aparc files. For my analysis, I now need the Desikan-Killiany Atlas ROI mask(s) (cortical and subcortical) in MNI or Talairach space. Is there any way to obtain these masks, e.g. by converting aseg/aparc files or by downloading them somewhere? Thanks a lot for your help. Best, Tim

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recon-all: making sure that brain.mgz will be in RAS orientation.
by Peled, Noam 14 Mar '19

14 Mar '19

Dear group, I ran recon-all on a T1 nii file, which is in LAS orientation. The brain.mgz turn out to be in LIA orientation. I've tried to convert the nii file to RAS (mri_convert --in_orientation LAS --out_orientation RAS ...), and rerun recon-all, but it didn't change the results. How do I make sure my output files will be in RAS orientation? Thanks, Noam

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Re: [Freesurfer] Welch's t-test for HOV violation
by Hannah CK 14 Mar '19

14 Mar '19

External Email - Use Caution Hi Dr. Greve, Sorry about that - I had followed the "Reply via email" link on the archive page instead of posting to the forum directly. Thank you for this response. Can extracting the means be done at the whole-brain level? If we get the means and variances for each group, I'm assuming we would need to use ROIs. Could you please clarify whether it's possible to extract means across the whole brain? Thank you, Hannah Re: [Freesurfer] Welch's t-test for HOV violation 2019-03-13 Thread Greve, Douglas N.,Ph.D. Hi Hannah, please include the previous correspondence so that we have context. Also, please remember to post to the list and not to us personally. thanks! doug On 3/13/19 10:52 PM, Hannah CK wrote: External Email - Use Caution Hi Dr. Greve, Thank you for this response. Can extracting the means be done at the whole-brain level? If we get the means and variances for each group, I'm assuming we would need to use ROIs. Could you please clarify whether it's possible to extract means across the whole brain? Thank you, Hannah ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Welch's t-test for HOV violation 2019-03-11 Thread Greve, Douglas N.,Ph.D. I used to have this about 20 years ago, but I stopped supporting it when it did not fit cleanly into the GLM ... The shortest route is probably to do two separate analyses with mri_glmfit, one for each group. This will output means and variances for each group. Then use fscalc to compute maps of the Welch's t. On 3/11/19 1:28 PM, Hannah CK wrote: > > External Email - Use Caution > > We are conducting t-test comparisons across groups in which there is a > large discrepancy in group sizes. HOV is violated. I've searched for > ways to run Welch's t-test in FreeSurfer (or a similar analysis that > does not assume homogeneity of variance) but am not finding one. > > Could anyone please advise on how to do this? > > Thank you.

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Freesurfer March 2019