Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

surfreg function
by Marina Fernández 20 Feb '20

20 Feb '20

External Email - Use Caution Hi experts, I am running the following command to create de average subjecto with Freesurfer v6.0: make_average_subject --out my_avg_subject --fsgd fsgd.txt Then, I want to do surface analysis with the thickness of each subject projected onto my_avg_subject. I would like to know if it is correct to run these commands before that statistical analysis: surfreg --s s_001 --t my_avg_subject --o my_avg_subject.sphere.reg mris_preproc --fsgd nfsgd.txt --target my_avg_subject --surfreg my_avg_subject.sphere.reg --meas thickness --srcfmt curv --hemi [l/r]h --out [l/r]h.fsgd.mgh Finally, I would use "[l/r]h.fsgd.mgh" file to do the thickness surface analysis. Is it correct? Should I run surfreg and use the output in mris_preproc?What is the advantage? Thank you very much!Marina-

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WM surface on pial surface and pial surface out of brain
by Bruno Pastorello 20 Feb '20

20 Feb '20

External Email - Use Caution Dear freesurfer developers, I have a subject that the wm surface is located where pial surface should be and pial surface is located out of the brain. I tried to use -FLAIR flag but the result is the same. Do you know what could be happening? How to fix this problem? thanks in advance Bruno Bruno Fraccini Pastorello Físico Médico | Ressonância Magnética | LIM44 Instituto de Radiologia do HCFMUSP Ramal: +55 11 2661-7619 bruno.pastorello(a)hc.fm.usp.br <xxxxxxx(a)hc.fm.usp.br> *Antes de imprimir* pense em sua responsabilidade e compromisso com o *AMBIENTE*.

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nopvc.nii.gz
by Marina Fernández 20 Feb '20

20 Feb '20

External Email - Use Caution Dear Freesurfer experts, I have compared the PVC uptake values of gtm.stats with the values of gtm.nii.gz (that I loaded with the function load_nii in matlab). I realized that the values in matlab are transposed, i. e., the first value in gtm.stats is the same that the last value in gtm.nii.gz and the same with the rest of the values. I couldn't find a way to check if the values are also in a transposed order in nopvc.nii.gz if I load it with load_nii in matlab. Could you tell me a method to verify it or confirm me that? Thanks again! Marina.

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Re: [Freesurfer] PetSurfer questions
by Soo-Jong Kim 20 Feb '20

20 Feb '20

External Email - Use Caution *Thank you Dr. Greve for your answer* I checked all about your comment. I have questions more. 1. I found that volumes or counts in gtm.stats.dat are for native PET space. If co-registered PET onto corresponding MRI(i.e. MRI space) is available using rbv.nii.gz from mri_gtmpvc, Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale (reference regions) for SUVR in PET space. What do you prefer or recommend? I'm not sure what you are trying to get. voxel volume or SUVR? *-> Yes. Voxel volume for SUVR analysis.* *I compared gtm.stats.dat from both GTM and RBV method.* *They were all same SUVR. I think region masks for gtm and rbv are same as pvc-masks, arent they?* 2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii --regheader because rbv.nii.gz is in different space. but when overlaid with them, registration is not correct. (WHY) rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space) I just wanted to use the pv-corrected image for image processing. and you also said, smoothing is required after PVC. (Surface or volume based smoothing (resonable). The RBV is in anatomical space, if you want to map it back to pet space, you need the registration file in the aux folder (not --regheader). *-> RBV has 0.5mm for voxelsize. even though I put image for input which has 1mm isotropic volume. * *You said that 'use in lta file in aux folder'. There are many lta files. So let me know what it is. * *- anat2bbpet.lta* *- anat2rbv.lta* *- bbpet2anat.lta* *- bbpet2pet.lta* *- pet2bbpet.lta* *- rbv2anat.lta* *my purpose is this. I want to map rbv.nii.gz to original T1MR space. Could you tell me how to do ?* *Thank you so much, Dr.Greve*

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-localGI, outer_smoothed surface defects?
by Octavian Lie 19 Feb '20

19 Feb '20

External Email - Use Caution Please see picture attached. Should I be concerned? I thought the outer_smoothed would always be "outer", but I see intersections with pia on one side. Thank you, Octavian

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BIDS 1.2.2 release and Genetic Information feedback
by Franklin Feingold 19 Feb '20

19 Feb '20

External Email - Use Caution We are excited to announce the release of BIDS version 1.2.2! This release enhanced the specification through additional clarifications and smaller fixes. The new recently released versions can be found at: https://bids-specification.readthedocs.io/en/stable/ along with the complete changelog<https://bids-specification.readthedocs.io/en/stable/CHANGES.html>. In addition, BIDS is calling a final round of comments on the Genetic Information extension proposal<https://github.com/bids-standard/bids-specification/pull/395>! Please review this extension proposal and leave your feedback - we aim to merge this extension soon! Shout out to the Genetic Information BIDS Extension Proposal leads: Cyril Pernet, Clara Moreau, Tom Nichols, and Jessica Turner! Thank you!

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mri_glmfit --no-prune
by Nasiriavanaki, Zahra 19 Feb '20

19 Feb '20

Hi Freesurferers I am running mri_glmfit on a group data using --no-prune flag. i 'm getting the below error. I appreciate if you could let me know what the issue is. Loading y from /autofs/space/oprah_001/users/zn025/looming_3T/group_levels/patients_20/loom.lh/aw/ces.nii.gz ... done reading. Saving design matrix to main2.wls/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 Found 149955 points in label. Found 149955 voxels in mask Saving mask to main2.wls/mask.nii.gz Reshaping mriglm->mask... search space = 74612.583051 ERROR: MRInormWeights: value less than or eq to 0. c=336, r=0, s=0, v=0 Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Problem running recon-all example from installation guide
by Andreas Vitikan 19 Feb '20

19 Feb '20

External Email - Use Caution Hello, I am trying to get the examples running as per the FreeSurfer installation guide. I initially got a recon-all not found error which turned out to be due to the lack of tcsh/csh, which I installed (I found this fix in the mailing list) and now get a different error. mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c /usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file or directory. I thought it might be related to permissions but running under sudo gives a different error. How do I fix this? - Andreas V.

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tktools: Bad CPU type on Mac OSX 10.15. Any workarounds or fixes?
by Chris Klink 19 Feb '20

19 Feb '20

External Email - Use Caution Hi Everyone, The 'Bad CPU type in executable' error for tktools like tksurfer has been a problem for me since Mac OSX 10.15 (Catalina). I know this is a 64/32 bit problem, but I'm wondering if there's a fix or workaround (other then 'use a different OS'). I tried the development version of Freesurfer (7.0.0b0) and noticed the tktools were gone there. Does this mean there's not a solution yet? Will tksurfer functionality be moved to Freeview? Very much related: is there another way to make cuts in surfaces for flatmap generation that doesn't require tksurfer and will work on Catalina? (It's not super urgent as I do have a different system available where things do work, but if there's a way this can work I'd like to know about it..) Thanks, -- Chris Klink

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Apply transformation
by Adam Rytina 19 Feb '20

19 Feb '20

External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam

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