Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

aparcstats2table subject space?
by Kasper Jessen 15 Feb '18

15 Feb '18

Dear FreeSurfer, When you extract e.g. thickness from the command aparcstats2table - is the data extracted from subject space? We need to know whether or not, we need to covariate for total brain volume. Bw Kasper Kasper Jessen, MD, PhD student Center for Neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper.jessen(a)regionh.dk<mailto:kasper.jessen@regionh.dk> ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den.

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V1 functional ROI
by Sarah Cole 15 Feb '18

15 Feb '18

Dear Dr. Douge, I am a little bit confused about creating function ROI in V1. Basically, I have some localizers that for some ROIs I need to find activated neurons in a specific contrast in native space and then create that ROI and map it to my experimental scans and extract their voxel data. I have used this command for right-FFA: funcroi-config -seg aparc+aseg.mgz 2007 -analysis eba-fba.native.rh -c faces-vs-objects -thresh 3 -sign pos -roi rh.surface.pSTS.faces-vs-objects.thr3.pos.roicfg -force But now, for V1 I am not sure what should I use. Is this correct? funcroi-config -seg aparc+aseg.mgz 400 -analysis eba-fba.native.rh -c faces-vs-objects -thresh 3 -sign pos -roi rh.surface.V1.faces-vs-objects.thr3.pos.roicfg -force I don't see a number in the lookup table for left and right V1. On the other hand, there are V1 labels in the label folder. I appreciate your help. Thanks

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Volume to Surface mapping looks great for Vols created in FSL but not SPM
by Rita Elena Loiotile 15 Feb '18

15 Feb '18

Hi, I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR). The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi}; It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis). I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command. I can attach pictures of the comparison if you'd like. Thanks in advance, Rita

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Removing labels after extending parcellation into white matter
by Michiko H. 15 Feb '18

15 Feb '18

Hi Freesurfer experts, I am wondering if it is possible to remove the original labels after extending the parcellation by 2mm into the WM for tractography? I don't wish to have tractography run on both sets of labels considering the algorithm would take into account the streamlines terminating at nodes defined by the labels so it doesn't quite make sense to count streamlines terminating at both the original label separately from the new label extending into the WM. I used the following command for growing the parcellation into WM: mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz Would appreciate help and suggestions! Thanks, Michiko.

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QDEC Set Up
by Martin Juneja 15 Feb '18

15 Feb '18

Hi FS experts, I have two population groups X1 (controls) and X2 (patients). I am interested in calculating impact of sex (F or M) on causing difference between both groups e.g. I am interested in following 4 contrasts: X1 (F) > X1 (M) X2 (F) > X2 (M) X1 (F) > X2 (F) X1 (M) > X2 (M) X1 (M+F) > X2 (M+F) Could you please provide any directions on how can I set this up in QDEC (if possible) and/or by command line? Thanks.

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FIR analysis
by Sarah Cole 15 Feb '18

15 Feb '18

Hi experts, I was wondering if there is any tutorial or example on FIR analysis. I don't know where to start. I need to look at the time course of some voxels. I have a localizer session and the main experiment. I am intending to find the ROIs in the localizer scans and then extract their time course activation in the main experiment scans. I have done the recon-all successfully. Then in my localizer scan, I did preproc-sess, mkanalysis-sess with FIR 6 24 flag, mkcontarst, and selxabg3. Now, I am lost. Sorry for my naiive question. Thank you, --SC

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inter-hemisphere registration on customised template
by Ting Qi 15 Feb '18

15 Feb '18

Dear Freesurfer experts, I am writing to ask how to do the surface-based inter-hemispheric registration based on the customised template, instead of fsaverage. I am planning to calculate the lateralisation index for each vertex, which means I should to use the symmetry template, for example, fsaverage_sym. However, the current issue is my participants are children. Therefore it would be better to put the individual data to the customised average template, which is already created by ANTS in my case. So I was wondering how to perform the symmetry registration on this created template? Thank you in advance. Cheers, Ting

2 1

Question regarding exporting subcortical segmentation to .nii ROIs for further analysis in SPM
by Simon, Joe 15 Feb '18

15 Feb '18

Dear Experts I just recently started using Freesurfer (implemented as a virtual machine on a Windows machine). After having completed the recon-all procedure, I now want to export the subcortical segementation as .nii images for further use in SPM. My aim is to have a ROI for each segmented subcortical structure. What would be the easiest way to do this? Any help is appreciated. Thanks a lot! Best regards, Joe ---------------------------------------------------------------- Dr. Dipl.-Psych. Joe Simon Universitätsklinikum Heidelberg Klinik für Allgemeine Innere Medizin und Psychosomatik Im Neuenheimer Feld 410 69120 Tel.: ++49(0)6221-56-38667 joe.simon(a)med.uni-heidelberg.de ----------------------------------------------------------------

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Re: [Freesurfer] Longitudinal TRACULA study
by Yendiki, Anastasia 14 Feb '18

14 Feb '18

Hi Donatas – All sounds fine. You can process single time points, and you can process subsets of time points if the DWI data from one of them is unusable. The T1 base template is only used as a reference space for longitudinal TRACULA, so it shouldn’t make a huge difference if one additional time point was used to generate that T1 base template (assuming of course that there wasn’t a huge morphological difference in that specific time point that would make the base template much different if it had been generated without that time point). Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Donatas Sederevicius <donatas.sederevicius(a)psykologi.uio.no<mailto:donatas.sederevicius@psykologi.uio.no>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, January 31, 2018 at 4:51 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Longitudinal TRACULA study Hi, I want to clarify some aspects longitudinal TRACULA processing before processing my data. For example, I have 3 timepoints of data of the same participant: sub101_01 sub101_02 sub101_03 All of these have structural and diffusion data (same scanner, same acquisition parameters). I processed structural data using FS longitudinal pipeline and got the following: base_101 sub101_01.long.base_101 sub101_02.long.base_101 sub101_03.long.base_101 Now I want to run longitudinal TRACULA processing. If all data is OK after quality checking (struct and DWI) I could set the configuration file as follows: set subjlist = ( sub101_01 \ sub101_02 \ sub101_03 ) set baselist = ( base_101 \ base_101 \ base_101 ) It turns out that DWI data of sub101_01 is extremely distorted and cannot be used for processing. Should I re-process struct data based on the last two timepoints or is it perfectly fine to use the base and long derived from all timepoints although I’m running tracula for the last two timepoints of DWI? In addition to that, is it fine to run longitudinal TRACULA on a list of subjects where some of them have only one timepoint of data and structural processing underwent longitudinal pipeline for that one timepoint? Thank you for your answers. Best, Donatas

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Status?
by John Davis 14 Feb '18

14 Feb '18

Hi. I'm completely stuck without more input from freesurfer experts. The email was about tracula. Could you confirm that you received my question and that I sent everything you requested? Thanks much. -- John Davis, PhD Cell: (520) 907-9769 jdavis(a)mrn.org

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