Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

Content of PET gtm.stats.dat file
by Donatas Sederevicius 14 Dec '16

14 Dec '16

Hello FreeSurfer Developers, I have run mri_gtmpvc command to perform PET PVC (partial volume correction) where input data has 4 frames (dynamic). The output volume as gtm.nii.gz has 4 frames as well which means that PVC was performed for each frame separately. However, gtm.stats.dat file has one value for each ROI. At first I thought it was the average of all frames but after manually comparing some ROIs it seems that the values in the file are taken only from the first frame of dynamic data. Is it the case or those values have another interpretation? Maybe it is the highest value across all frames? In addition, is there an easy way to get the same file where the values would be the average across all frames?

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-FLAIRpial; T2 SPACE
by Octavian Lie 14 Dec '16

14 Dec '16

Dear All, Our MPRAGE and T2 SPACE FLAIR sequences are acquired at times during two different scans, and the MPRAGE seq further gets reoriented in a pipeline upstream of the Freesurfer step. For best results, does the FLAIR volume have to be reoriented (and resliced) in a rigid registration to the MPRAGE before recon-all -all stage, or it does not matter? Thank you, Octavian

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Label creation
by Leyton Moscoso, Cristian Eduardo 14 Dec '16

14 Dec '16

Hi Freesurfer's experts Is there an easy way to create automatically a circular label with a radius centered on a vertex with predifined RAS/Tailarach coordinates on the fsaverage surface? Thanks Cris

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5.3v migration
by Eduard Vilaplana Martinez 14 Dec '16

14 Dec '16

Dear FS experts, We are planning to update all our subjects from de 5.1v to 5.3v. Our subject database processed with the 5.1v is really big so we are thinking about ways to not start over new. Is there any way to take advantage of the 5.1v segmentations? We have been thinking about using a dilated version of the already corrected 5.1v aparc+aseg as a brainmask for the new segmentation. Any ideas would be appreciated. Is there any standarized way to carry out this kind of process? And is there any way to take profit from the wm segmentation of the older version? Thanks in advance, Edu V.

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Reminder to cite FreeSurfer in your OHBM abstract
by Douglas N Greve 14 Dec '16

14 Dec '16

Hi All, as you finalize your OHBM abstract, remember to cite FreeSurfer. There is a box to check that you used FreeSurfer when you submit your abstract, but also please put some indication in the text that you used FreeSurfer if you can. If you have room to put in a citation, there are several below you can use. thanks! doug 1999. Dale, A.M., Fischl, B., Sereno, M.I., Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction. Neuroimage 9, 179-194. 1999. Fischl, B., Sereno, M.I., Dale, A.M., Cortical surface-based analysis. II: Inflation, flattening, and a surface-based coordinate system. Neuroimage 9, 195-207. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Brighter image at baseline vs. follow up using longitudinal processing stream
by Tamara Tavares 14 Dec '16

14 Dec '16

Hello, I am in the process of checking the alignment of my participant's baseline and followup scans to the template scan using the norm.mgz files. I notice that sometimes the image appears brighter in the first scan vs. the second follow up scan. Is this problematic? I don't see any clear distortions or translations when I compare the participant's scan to the template. Thank you in advance for your help! Tamara

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Longitudinal base creating in version 5.1 vs 5.3
by Allison Rainford 14 Dec '16

14 Dec '16

Hi FreeSurfer team, My lab is looking at longitudinal data across 5 time points for each subject. All of our time points have been edited in version 5.1 for consistency. However, I have run into an issue when trying to create the bases for these subjects in this version due to a memory allocation problem. It appears that 5.1 cannot allocate enough memory to store the temporary files for each of these time points and consequently errors out during the registration stage with this message: Iteration(f): 2terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc I also tried creating the base using a memory flag (-m) to allocate more memory but had no luck in those attempts. I tried creating the base in version 5.3 and this ran successfully. However, because this is a longitudinal data set ran in version 5.1, it's problematic that the jobs crash in 5.1. Is there anyway to allocate sufficient memory in 5.1? Thank you, Allison Rainford Research Study Assistant Cognitive Neurology and Alzheimer's Disease Center Northwestern University 320 East Superior Street Searle 11-579 Chicago, Illinois 60611 Email: allison.rainford(a)northwestern.edu

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recon-all -s <subj> -localGI
by André Schmidt 14 Dec '16

14 Dec '16

Dear experts I am trying to compute the local gyrification index but I am not sure how I have to do the following: "You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script." Can you please quickly help me what I need to type in the terminal to do this in order to run recon-all -s <subj> -localGI? Many thanks for your help! Best wishes André

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dimensions of the segmented MRI
by Aya Kabbara 14 Dec '16

14 Dec '16

Dear freesurfer team, Do we have the option when using "recon-all" command to predefine the dimensions of the segmented MRI? (for example 145*174*145 with 1.25 mm). Thank you a lot, Aya

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question white matter analysis
by tom parker 14 Dec '16

14 Dec '16

Dear FreeSurfers, Thanks for the previous reply on what the white.K and white.H are. I would like to make an analysis in Qdec using one of these measures. However, I didn't find much information online so I would like to ask you 3 final things: 1. Which of the two measures (mean, gaussian) is more suitable for an analysis of white matter volume/curvature? 2. How can I apply some smoothing to the white.K and white.H files to be able to make an analysis in Qdec? 3. Should I include ITV as a covariate in these analyses? Thank you so much!

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Freesurfer December 2016