Freesurfer May 2016

freesurfer@nmr.mgh.harvard.edu

135 participants
197 discussions

mris_preproc - srcsubjreg
by Makaretz, Sara Johanna 01 Jun '16

01 Jun '16

Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as the default srcsurfreg when the target is not fsaverage - see below Thanks for any info! (not urgent) On 2016-5-24, 11:30, "Z K" <zkaufman(a)nmr.mgh.harvard.edu> wrote: >Good question, and I dont know the answer. mris_preproc is Dougs baby so >I suggest just posting this question to the list with "mris_preproc" in >the subject, and I bet he will give you the answer. > >-Zeke > >On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote: >> Hi Zeke, >> >> I am running some surface glms where targ is a patient surface. The help >> says --target TargetSubject (requires ?h.TargetSubject.sphere.reg), and >> I was getting errors because dev-default mris_preproc wanted >> mri_surf2surf to have srcsurfreg = >> $SUBJECTS_DIR/$srcsubject/surf/$h.$TARGSUBJ.sphere.reg >> >> But mris_preproc in 5.3 let me do target = patient surface with no extra >> surf reg files or extra flags to get mri_surf2surf to use srcsurfreg = >> $SUBJECTS_DIR/$srcsubject/surf/$h.sphere.reg >> >> I had been running this with 5.3: >> mris_preproc \ >> --target $TARGSUBJ \ >> --hemi lh \ >> --meas thickness \ >> --fsgd file.fsgd \ >> --out lh.output.mgh >> >> And I was about to email freesurfer@nmr but "for fun" tried adding >> --surfreg sphere.reg which got mris_surf2surf to use the right reg >> files. So now I'm selfishly trying to figure this out - do you know what >> prompted the switch from sphere.reg "opt-out" to sphere.reg "opt-in"? >> Aka why sphere.reg is non-default when the target is non-fsaverage? Did >> that make sense? I know there must be some reason, so I really want to >> know a bit more so I can stay sane when old scripts break. >> >> Thanks for any info! Sorry to bother you! >> Sara >> >> >> >> >> >> >> Outputs from the FS-dev one: >> >> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $ >> .... >> Src lh $TARGSUBJ.sphere.reg >> Trg lh sphere.reg >> .... >> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg >> $TARGSUBJ.sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg >> sphere.reg --etcetcetc >> .... >> ERROR can't find $SUBJECTS_DIR/$SRCSUBJ/surf/$TARGSUBJ.sphere.reg >> because I never made it >> >> >> >> Outputs from the FS-dev one with fsaverage as the targ subj: >> >> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $ >> .... >> Src lh sphere.reg >> Trg lh sphere.reg >> .... >> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg >> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --etcetcetc >> .... >> mris_preproc finds everything, runs no problem >> >> >> >> Outputs from the FS-5.3 one: >> >> $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ >> .... >> Src lh sphere.reg >> Trg lh sphere.reg >> .... >> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg >> --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg sphere.reg --etcetcetc >> .... >> mris_preproc exits with no errors because everything exists >> >> >> >>

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Tracula skip steps
by Jacobs H (NP) 31 May '16

31 May '16

Dear FreeSurfers, The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3. I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz I have also filled in the configuration file, canceling out the things I don't need and then I tried to run: Trac-all -intra -c <configuration file> Unfortunately, it does not work, it says: dcmlist: subscript out of range I do not have the original files... is there a way that I can get the script working? Many thanks. Heidi

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Extracting White Matter Structures without using Tracula
by Syeda Wajiha Maryam 31 May '16

31 May '16

Hello Freesurfer experts, I am looking to extract certain white matter pathways (for instance, the superior longitudinal fasciculus, uncinate fasciculus) with freesurfer which I believe are affected by Alzheimer's Disease. But it seems that these can only be obtained by performing tractography using Tracula. I was wondering if there was some other way to obtain the labels for these structures without having to do so? Thanks in advance. Regards, Maryam

2 2

WM & GM Parcellation Edit
by Limachia, Gaurang (NIH/NINDS) [F] 31 May '16

31 May '16

Hi freesurfer community, We are checking to see the accuracy of our subjects’ white and gray matter parcellation. We have found that for some subjects the contour lines for white matter surface and pial surface are somewhat inaccurate, and have been making modifications using the tutorials. Specifically, we made changes to the white matter wm.mgz file; this however did not alter the contour lines. We also used control points, and were able to see changes to the white matter surface contour lines using this approach. How do you recommend that we proceed to obtain the most accurate results? Should we continue making changes to the wm.mgz file as well as adding control points, or is it sufficient just to add control points? I am attaching a screen shot which shows changes to the contour lines after we added control points. Best Regards, Shyam [cid:93CEA6F8-6B62-4483-985C-F540EDDBD2D7] [cid:C981D3FE-7C43-4073-A91F-F26CEDDC4145]

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working with cluster annotations in fs-fast
by Abigail Noyce 31 May '16

31 May '16

Hi folks, I'm trying to split a cluster from mri_glmfit-sim into two separate regions. (Ginormous blob of activation across multiple structures of interest...) I've gotten to the point of generating a new annotation with the separate labels for my separate regions, but am stuck getting a "cluster size" for the new labels. It looks like one can't use mris_anatomical_stats on fsaverage... but something like that must be happening inside of mri_glmfit-sim to get cluster sizes? What's the best way to get these values for my new annotation? (Or is this a terrible idea for some reason I haven't yet considered?) Thanks! Abby Noyce -- Abigail Noyce, Ph.D. Department of Psychological & Brain Sciences Boston University anoyce(a)bu.edu

2 1

recon-all with input T1s at different resolutions
by Satrajit Ghosh 31 May '16

31 May '16

hi folks, does recon-all work if the input T1s for the same participant have different resolutions? (i don't have a dataset to test, but trying to debug some issues another group has been having). cheers, satra

4 7

WM & GM Parcellation Edit
by Limachia, Gaurang (NIH/NINDS) [F] 31 May '16

31 May '16

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WM & Gray Matter Parcellation Edit
by Limachia, Gaurang (NIH/NINDS) [F] 31 May '16

31 May '16

1 0

Algebraic operations with scalars
by Francesco Cardinale 31 May '16

31 May '16

Dear Freesurfer experts, I would like to make some algebraic operations with scalars, such as ?h.thickness or sig.mgh. They are referred to the same surface, of course. How can I export the thickness values to a spreadsheet? (?h.thickness 2 table) How can I export the significance values to a spreadsheet? (sig.mgh 2 table) All my best Cico Francesco Cardinale, MD Neurosurgeon "Claudio Munari" Centre for Epilepsy and Parkinson Surgery - Ospedale Niguarda "Ca' Granda" Piazza dell'Ospedale Maggiore, 3 - 20162 - Milano - Italia <x-apple-data-detectors://0/0> phone 0039 02 64442917 <tel:0039%2002%2064442917> fax 0039 02 64442868 <tel:0039%2002%2064442868> e-mail francesco.cardinale(a)ospedaleniguarda.it <mailto:francesco.cardinale@ospedaleniguarda.it>

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Re: [Freesurfer] Manual segmentation issues
by maryam_koochaki 31 May '16

31 May '16

Hi Antoine,Have you tried control points seeding, I usually place the control points right behind the surface in trouble areas so seeded points would push the surfaces forward.Maryam Sent from my Samsung Galaxy smartphone. -------- Original message --------From: Saturne Fox <saturne.fox(a)gmail.com> Date: 2016-05-31 1:20 AM (GMT-08:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Manual segmentation issues Dear freesurfer community, These days I am manually editing some data and this subject is giving me such a hard time. In fact I would like the near-to-cortexartefacts at the top right hand corner to be excluded from the surface but even after changing the intensity of the wanted part to 255 and the one of the excluded parts to 1 (which is nevertheless not visible on these images) the surface is still not what I would like it to become. In adition to editing the wm.mgz file, I also modified the aseg.presurf file to exclude these parts and I re-runned the -normalization2 and -maskbfs flags to generate new brain.mgz and brain.finalsurfs.mgz files. Any idea why these modifications are not affecting the surface ? Best regards, Antoine

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Freesurfer May 2016