Freesurfer

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19 participants
30088 discussions

questions about batch running longitudinal data using long_submit_jobs on cluste
by Huang, Yiting 21 Feb '20

21 Feb '20

Hi there, I am trying to run some longitudinal data using freesurfer long_submit_jobs command on cluster. I have double checked my directory and files setup according to freesurfer longitudinal preprocessing wiki:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts. And it seems there is no problem with my setup. However, when I run the command it keeps sending me error as below: launchpad:yh917[21] long_submit_jobs --qdec long.qdec.table.dat --cdir $PWD/../ --cross --base --long --pause 5 --max 200 --queue max100 File "/usr/local/freesurfer/stable6_0_0/bin/long_submit_jobs", line 94 print "job submission failed, maybe unknown host "+hostname ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("job submission failed, maybe unknown host "+hostname)? I can't figure out the reasons. Any help please? Thanks, Yiting

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bias correction on 7T MEMPRAGE
by Barletta, Valeria 21 Feb '20

21 Feb '20

Dear Freesurfers, I am trying to apply the bias correction on the 7T MEMPRAGE through the unified segmentation algorithm on SPM12, as a primary step to do the submillimetric recon on Freesurfer, as you suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon For some reason, I cannot set the Bias FWHM to 18 on the SPM12 interface. Also, not sure how to use the 5D image that I obtain from the process. Have you ever done this before? Any tips? Thanks a lot, Vale

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how to perform No Partial Volume Correction for PET using PETSURFER
by Kate Marvel 20 Feb '20

20 Feb '20

External Email - Use Caution Dear All, I would like to perform no partial volume correction of PET using PETSURFER. The steps followed in doing this is shown below: gtmseg --s Patient_1 mri_concat Patient_1_pet.nii.gz --mean --o Patient_1_pet_tac_vol_mean.nii.gz mri_coreg --s Patient_1 --mov Patient_1_pet_tac_vol_mean.nii.gz --reg Patient_1_pet_registration.lta --threads 4 mri_gtmpvc --i Patient_1_pet.nii.gz --reg Patient_1_pet_registration.lta --no-tfe --psf 0 --seg gtmseg.mgz --o Patient_1_gtmpvc.output.psf6 I would like to know whether these steps suffices for a no partial volume correction. Thanks. -- kate

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correlation analysis
by Raffaele Dubbioso 20 Feb '20

20 Feb '20

External Email - Use Caution Dear FS team, in my analysis I'd like to correlate two variables such as cortical myelination and neurophysiological metrics, regressing-out thickness and age of the subjects. I have only one group. My FSGD file should be: GroupDescriptorFile 1 Title NF_Myelin Class Main Variables NF age Input fs_VF Main 1.57 46 Input fs_RF Main 1.5 22 Input fs_SE Main 1.09 30 ..... My intercet2.mtx should be: 1 0 0 0 My slope2.mtx should be: 0 1 0 0 This is my line command: mri_glmfit --y rh.t1t2ratio_20_fmed_3sm_decurv.fsavg.mgh --fsgd T1T2_NF_AGE_HS.fsgd --pvr lh.thickness_20.fsavg.mgh --C intercept2.mtx --C slope2.mtx --surf fsaverage lh --o lh_NF_AGE_T1T2_thickness Is everything ok? Thanks a lot Raf

2 1

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-

2 1

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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