Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

how to interpret a change in area of 0.004 mm² per year?
by Lars M. Rimol 09 Sep '14

09 Sep '14

Hi, I have performed a longitudinal analysis using the lme module in FreeSurfer, with this model: *intercept(random effect) + centered age + group + group x centered age + sex* I tested the effect of time with this contrast vector [ 0 1 0 0 0 ]. Dependent variable is area. Here, mapping the second beta means mapping the effect size for (change over) time. In the beta map, I find values from 0 to 0.004. I would interpret that to mean that local area shrinks by at most 0.004 mm² per year in the reference group. But I'm not 100% sure about the biological (or geometrical) meaning of that. Can I interpret this literally as the mean yearly shrinkage of the three triangles surrounding a given vertex, the average of whose area comprises the area score of the vertex, being 4/1000 mm? Of course, these maps are smoothed with 30mm, so the real spatial resolution is nowhere near this.... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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Using fieldmap to correct EPI distortions
by Reza Rajimehr 09 Sep '14

09 Sep '14

Hi, I have a basic question, but the answer can be useful for others as well. I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So: My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan) My EPI data: fmc.nii.gz files in run folders Now I have three questions: 1) How can I unpack the fieldmap data? An example command ... 2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an example command would be very useful. 3) How will the undistorted volumes be used later on in the FS-FAST analysis stream? Your help would be very much appreciated. Thanks, Reza

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freesurfer commands from MATLAB
by Barbara Kreilkamp 09 Sep '14

09 Sep '14

Dear Freesurfers, Is there a way of calling freesurfer-scripts from within MATLAB? I know there are some setups needed to make MATLAB understand where it can find the commands (I have done this before with FSL). I am using bash, and when I type the Freesurfer commands in a terminal by hand, they work. So I am guessing it must have to do with setting up the environment: freesurf_path ='Applications/freesurfer'; setenv('FREESURFDIR',freesurf_path) setenv('FREESURFOUTPUTTYPE','NIFTI_GZ') curpath = getenv('PATH'); setenv('PATH',sprintf('%s:%s',fullfile(freesurf_path,'bin'),curpath)); Thanks a lot for any help, Barbara

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Re: [Freesurfer] QCACHE error
by Gayane Aghakhanyan 09 Sep '14

09 Sep '14

Dear list, I'm running longitudinal two stage model as is described in the tutorial here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel First, I've proceeded with longitudinal pipeline all my data, second, I've created longitudinal qdec table, and then, I've started to qcache my data, which after few seconds ends up with error: SUBJECT template_malfara fwhm 0 computing PC1 mris_calc -o /home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh ./tmp-template_malfara_lh_thickness_Dkx9j1/beta1.mgh div ./tmp-template_malfara_lh_thickness_Dkx9j1/tp1.mgh Saving result to '/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/template_malfara/surf/lh.long.thickness-pc1.fwhm0.mgh' (type = MGH ) [ ok ] ERROR 1 : mris_calc compute percent change (pc1) problem? Please, could you give me a hint how I can overcome this error? -- Gayane Aghakhanyan, MD PhD candidate, Institute of Life Sciences Scuola Superiore Sant'Anna Piazza Martiri della Libertà Pisa 56127, Italy tel: +39 327 7013870 email: g.aghakhanyan(a)sssup.it

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Tracula reconstructed tracts quality
by Peggy Skelly 09 Sep '14

09 Sep '14

Hello Tracula experts, I was wondering if you could comment on the quality of the tracts reconstructed with our 1.5T data. These 2 files are from the same subject at 2 timepoints, processed in the longitudinal stream. Is much of the non-smooth look of the tracts due to the resolution of the dwi scans (1.8x1.8x4mm)? What could be the source of the diagonal lines/gaps in the tracts seen in tp1 when viewed from above? Thanks, Peggy

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hippocampal subfields: from posterior to binary masks
by Luigi Antelmi 09 Sep '14

09 Sep '14

Dear list members, as you know, the hippocampal subfields given back by FreeSurfer (posterior_left_CA1.mgz, posterior_left_CA2-3.mgz, etc.) are posterior probability maps in the range [0-255] (i.e. [0-1] with 8 bit of quantization). Although there is a way to calculate the volume ( kvlQuantifyPosteriorProbabilityImages) that operates by summing up all the greyscale values <https://github.com/neurodebian/freesurfer/blob/master/GEMS/kvlQuantifyPoste…> (an equivalent method is to integrate the histogram over the range 0-255), to my knowledge there is no freesurfer's routine able to extract a binary mask out of the posterior probability map. What procedure do you use or suggest? I think there are two possibilities here. 1) As written in the paper from Van Leeput et al. <http://www.ncbi.nlm.nih.gov/pubmed/19405131>, I can *"assign each voxel to the label with the highest posterior probability"*. Althought I'm wondering why such a thing, documented in the paper, has not been implemented yet, I do not think this is the right way to do it because this procedure do not make any distinction between low probability voxels and high prob ones. 2) Threshold the subfields such that the volumes of the thresholded mask will equal those calculated by integrating the histogram on the domain 0-255; Formally, find *t* such that: where *H* is the histogram of the subfield. I prefer the second option because here low prob values are discarded, and because one can apply the equation to a rigid transformed subfield, thus limiting the partial volume effect of the resampling. What do you think about? Luigi.

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Brodmann Area stats to table
by Silas 08 Sep '14

08 Sep '14

Hi guys! Is there an easy way to get Brodmann Area stats to table like there is for aseg and aparc stats? Thanks! Silas PS. I looked the question up and it was answered in 2011 - I was just wondering if you guys made an easy way around the problem since then :)

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help extracting Brodmann areas masks
by David Provencher 08 Sep '14

08 Sep '14

Hi, I am new to freesurfer and I am trying to figure our how to extract 3d masks in native space for the visual cortex (BA 17,18,19) of individual subjects. I have looked at other threads similar to this, but there are still a few things I can't figure out in generating the masks (the conversion to native space should be fine). 1- I ran recon-all and I have V1, V2 and MT labels. My knowledge of brain anatomy is very limited, but if I understand correctly, this equates to BA 17, 18 and V5, so I don't have access to all of B19 (V3, V4 and V5), right? 2- I managed to convert V1, V2 and MT labels to 3d masks using mri_label2vol and it seems to work at first glance when I looked at the generated file with freeView. However, I read in the mailing list that mri_label2vol produces "patchy" volumes and that it is preferable to use mri_aparc2aseg instead. That's what I can't figure out. From what I understand, mri_aparc2aseg aims to map the surface labels of interest to the segmented volumes? I tried doing the following (I altered some file names/paths for readability): # convert labels to annotation (outputs lh.myAnnot.annot & rh.myAnnot.annot)) mris_label2annot --s <subject> --h lh --l lh.V1.label --l lh.V2.label ---l lh.label --ctab BA.ctab --a annot mris_label2annot --s <subject> --h rh --l rh.V1.label --l rhV2.label ---l rh.label --ctab BA.ctab --a annot # convert to volume mri_aparc2aseg --s <subject> --annot myAnnot.annot --o lh.asegTest.mgz When I look at the asegTest.mgz file in freeView, I only see segmented cortical volumes and I can't see anything related to V1, V2 or MT, so I assume that I don't use mri_aparc2aseg correctly, but I can't manage to make it work. Any help would be appreciated! David

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Re: [Freesurfer] does Tracula correct for CSF contamination
by Anastasia Yendiki 08 Sep '14

08 Sep '14

Hi Laura - Apologies, I just found your email and realized I hadn't answered earlier. Which tract are you concerned about being contaminated by CSF? a.y On Wed, 27 Aug 2014, Laura Christine Anderson wrote: > Dear Tracula users, does anyone know whether or not Tracula uses any corrections for CSF > contamination? > > Thanks for your time, > Laura > -- > Laura Anderson, B.A. > Graduate Student > Clinical / Developmental Psychology > University of Maryland > College Park, MD 20742 > BPS 0112 > >

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Question about "mri_convert"
by Nooshin Zadeh 08 Sep '14

08 Sep '14

Dear FreeSurfer experts, I get a new message when I use "mri_convert" command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file. *mri_convert "/M1/t1_se_ax_5/IM-0004-0001.dcm" "/FS/M1/mri/orig/001.mgz"* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin

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Freesurfer September 2014