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Re: [Freesurfer] TRACULA: Motion measures only
by Yendiki, Anastasia 16 Jun '17

16 Jun '17

Yep, you can use the dmri_motion command. Run it without any arguments to see usage info. It needs: * Your original, unprocessed DWIs * b-value table * Output from your FSL eddy correction (*.ecclog from eddy_correct or *.eddy_parameters from eddy) Hope this helps, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Buckless, Colleen" <Buckless(a)kennedykrieger.org<mailto:Buckless@kennedykrieger.org>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, June 16, 2017 at 10:22 AM To: "'freesurfer(a)nmr.mgh.harvard.edu<mailto:'freesurfer(a)nmr.mgh.harvard.edu>'" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] TRACULA: Motion measures only Hi All, I have already preprocessed data in FSL and only want to use TRACULA to get the motion measures to match subjects based on motion. Is there any way I can get out the motion measures without doing all of the other preprocessing steps in TRACULA? Thanks, Colleen Buckless ________________________________ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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TRACULA: Motion measures only
by Buckless, Colleen 16 Jun '17

16 Jun '17

Hi All, I have already preprocessed data in FSL and only want to use TRACULA to get the motion measures to match subjects based on motion. Is there any way I can get out the motion measures without doing all of the other preprocessing steps in TRACULA? Thanks, Colleen Buckless ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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FA ROI analysis using 6-gradient-dir DWIs
by Yong Li 16 Jun '17

16 Jun '17

Dear Bruce, Dear Anastasia, I would like to investigate white matter changes in a group of elderly patients. The acquired DWI data are 6-gradient-direction+1-non-DWI images by a clinic routine (not by me unfortunately). The meaningful analyses may be ROI-based DTI model considering FA, MD etc. measures to perform group comparisons. Subcortical ROIs like thalamus, putamen in aseg as well as white matter bundles like *h.cst_AS etc. in TRACULA are of my research interests. I would like to kindly ask the following questions: 1. To compute FA/MD of thalamus for instance, shall I simply apply individual thalamus mask extracted from aseg to wmparc then output the results in .stats files? 2. TRACULA analysis works with my DWI data (6 gradient-direction) so I could extract masks of the 18 tracts, which serve as ROIs in the FA/MD group analysis. I wonder whether there exists a better alternative to extract fiber bundle masks? The practical issue is that it takes >20 hours to process single patient and I have hundreds and it's accumulating. 3. Is there a new development to enable adding new labels to the TRACULA atlas? I would like to include Corona Radiata, Inferior Fronto-Occipital Fasciculus, Olfactory Tract etc. So far I only found this post to do it manually: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31955.html. Thank you all very much in advance! Kind regards, Yong

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web image preprocessing
by tom parker 16 Jun '17

16 Jun '17

Dear Freesurfer experts, Does anyone know if there is a web portal where i can upload my T1 images to preprocess them with freesurfer and download the preprocessed files? Thank you so much!

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Design matrix for local gyrification index in QDEC
by marco mcsweeney 16 Jun '17

16 Jun '17

Dear all, I have a quick question regarding the appropriate design (DOSS, DODS, SOSS, SODS) to be used with QDEC when comparing LGI values for 2 groups (patients and healthy controls). I have noted that a number of publications have used DODS when comparing LGI values between 2 groups while controlling for age and gender, but I was just wondering if this is the correct design to use for this type of analysis. I am aware that only DODS and DOSS can be used with QDEC but that it may be possible to use SOSS or SODS with mri_glmfit. I would like to be 100% sure about which is the most appropriate design to use. I have 2 groups with 29 subjects in each group (N = 58). The reason I ask this is because I am wondering whether it would be better to use SOSS (same offset same slope) when looking at LGI because, as I understand it, cortical folding patterns are roughly determined in the first few months of life and remain relatively stable into adulthood, unlike cortical thickness which is much more dynamic. If the results of this analysis are significant after FDR correction I would assume that this suggests that cortical folding patterns are indeed different in the 2 groups. Any help or advice on this would be greatly appreciated. Thank you so much in advance. BW Marco

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substract images
by John Anderson 15 Jun '17

15 Jun '17

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Freesurfer parcelations of cortical regions in TrackVis
by Leyton Moscoso, Cristian Eduardo 15 Jun '17

15 Jun '17

Hi Freesurfer’s and TrackVis experts I am wondering if there is a way to import cortical parcelations mapped on a T1 image in TrackVis. I tried loading segmentation in TrackVis, but this does not allow me to see all parcelations in T1 as I can be done in Freeview. In TrackVis I need to upload them one by one. Thank you Cris Dr Cristian Leyton M Research Fellow in Neurology Department of Neurology Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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viewing 3D surfaces
by Michael Davies 15 Jun '17

15 Jun '17

Hello, i am having problems accessing the 3D surfaces of my data. Is there any advice you could provide for me please? bash-4.1$ freeview -f \ > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.inflated:visible=0 \ > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.white:visible=0 \ > /projects/pbic1030/Michael/subjects/Subj1/fsaverage/surf/lh.pial \ > --viewport 3d bash: freeview: command not found Kind regards, Michael

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bvals and bvecs for tracula v6
by Marissa Pifer 15 Jun '17

15 Jun '17

Hi freesurfers, I recently updated my freesurfer version from 5.3 to 6, and I'm running into a problem with the tracula dmrirc.example file. In the dmrirc.example file for v5.3, it required just the bvals and bvecs in a text file in the correct format. For v6, it now requires a bval files, bval list, bvec file and bvec list. Could you give me an example of what the bval list and bvec list would look like? I'm not sure what the difference is, and I've tried a few different things but cannot get tracula to run correctly due to there being an error with these inputs. Marissa

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mris_anatomical_stats and cortical thickness
by Taylor Hilton 15 Jun '17

15 Jun '17

Hi all, I’m trying to extract individual cortical thickness values using the output of the annotation file from mri_glmfit-sim. This worked well for the left hemisphere, we got values that were significantly different between groups we had specified in mri_glmfit, but for the right hemisphere we get all values of 0 for the cortical thickness and mean curvature. I’ll post the commands I’m running below. Essentially I’m attempting to take the annot file from mri_glmfit-sim, convert it to a label, then put that label onto a subject (which may or may not be necessary), and pull out the anatomical stats using that label. Below is the example code for one subject. I did also confirm that the initial annot file, and the final subject label both sit on the right hemisphere when loading them up in freeview. I’ll also attach the summary file from mri_glmfit-sim for the cluster and a sample recon-all log. Any help is appreciated! - Taylor H. Lab Data Coordinator LRDC, University of Pittsburgh mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts --annotation archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1 mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label --trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh --regmethod surface mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >> s72064/scripts/rh-cluster001.txt Using TH3 vertex volume calc Total face volume 228346 Total vertex volume 224557 (mask=0) table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 86 64 179 0.000 0.000 0.108 0.018 1 0.1 s72064/label/rh.cluster-001.label

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