Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

fix topology issue
by miracle ozzoude 01 Aug '17

01 Aug '17

Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul

3 13

RBV PVC: Saving output file before upsampling
by SudEEpti 18 Jul '17

18 Jul '17

Hello, Is there a way to save the PVC (RBV) output in native PET resolution, before upsampling? Would you also be able to share the command that is used for upsampling? I would like to play with a different type of interpolation. Thank you very much. Su

3 5

bbregister vs spmregister vs mri_coreg
by John Anderson 06 Jul '17

06 Jul '17

Dear Freesurfer experts, I see that the tool "mri_coreg" has been implemented recently in Free Surfer 6 and I really wanted to know what are the differences between the registration tools "bbregister", " spmregister" and "mri_coreg"! Kindly: 1. Are these tools similar? if not what are the differences ? 2. Is there any preference of using a tool over the others for specific type of data. For example: A. If I want to register FA map to T1 image which tool is more robust? B. if I want to register FA map to MNI space which tool is more robust? I highly appreciate your input on this! John

2 3

Raw Cortical thickness values
by Muhammad Naveed Iqbal Qureshi 06 Jul '17

06 Jul '17

Dear Community, I need to know how can I read the numeric cortical thickness values from freesurfer processed files. (as there are too many in the surf folder) Thank you. Best Regards Naveed

2 2

Average myelination within ROI
by SHAHIN NASR 06 Jul '17

06 Jul '17

Hi Surfers, I want to measure the average amount of myelinations within my ROI(s), I have already generated my myelination maps on surfaces (e.g. lh.myelin_ProjFrac0p5.nii ). Then I used mri_segstats as below: mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1 --sum V1_Stats.txt --accumulate but the numbers don't make any sense. For instance: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 125261 82573.4 Seg0000 110280.4453 0.2922 -5.5000 51.0000 56.5000 2 1 1138 764.8 Seg0001 941.0988 0.1572 0.2675 1.4203 1.1527 How can mean=941.0988 when the max=1.4203 ??? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

Difference between -autorecon2-wm and -autorecon2-noaseg ?
by Makaretz, Sara Johanna 12 Jun '17

12 Jun '17

Hi, I'm using FS v6.0 stable. Is there any difference between running recon-all with -autorecon2-wm or -autorecon-noaseg? It looks like both are starting at -normalization2 and running through the rest of autorecon2 with no changes to inputs/args compared to "regular" -autorecon2. Is this true, and can I use -autorecon2-wm and -autorecon2-noaseg interchangeably? https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 Thanks! Sara

1 2

Statistical analysis
by Laura Ferrero Montes 11 Jun '17

11 Jun '17

Dear FS team, Thank you very much for your help. Just a few more questions. I want to perform a statistical analysis between two groups:controls and patients, using age and IQ as covariates. First I have to test if there is an interaction between group and covariate using DODS. My questions are: Q1) Do I have to test age and IQ separately, or together? Q2) In case that there is not interaction in any of the covariates, can I use the same FSGD file but do I have tu run it as DOSS? How it could be done? I would appreciate if you could give me some hints or examples about the matrices and contrast files that I must use. Thank you, All the best, Laura

3 10

[TRACULA] Issue with registration to diffusion space
by Ostrowski, Lauren 08 Jun '17

08 Jun '17

Hello experts, I'm in the midst of processing a series of subjects for analysis in TRACULA, and have come across one subject which doesn't seem to be registering correctly. I edited the registration manually using tkregister2 (photos "lowb_brain_anat" and "T1" attached), and then ran bbregister myself using this new registration. I then re-ran TRACULA -prep starting at the inter-subject registration, skipping the steps up to and including intra-subject registration (using the new files from my manual bbregister). However, the registration still doesn't seem to have completed correctly (see photos "aparc+aseg_vs_FA_cor and "aparc+asef_vs_FA_sag"). Any advice as to why this bad registration could still be happening and how to correct it? Thanks, Lauren Ostrowski

3 13

F and p- values for non sig findings
by Lim, Lena 08 Jun '17

08 Jun '17

Dear Freesurfer experts, I tried to do a group x gender interaction in QDEC and there is no sig interaction, but how do I get the F or T and P values please as requested by the reviewers? Many thanks, Lena

2 2

7T recon
by Hibert, Matthew Louis 07 Jun '17

07 Jun '17

Hi All, I reconstructed 20 subjects with a 750um isotropic MPRAGE collected at 7T and while most look good, 4 of the subjects have a similar section of the left STG removed from the final surfaces (picture attached). In all 4 subjects the entire left STG is included in the wm.mgz and lh.orig.nofix (red), but a portion has been removed in lh.orig (yellow), so the problem seems to occur in the -fix stage of autorecon2. How can I go about correcting this issue? Thanks, Matt

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Freesurfer May 2017