Freesurfer

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30099 discussions

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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Functional connectivity
by Martin Scherr 08 Sep '14

08 Sep '14

Dear Freesurfer experts, We are trying to perform a resting state functional connectivity analysis (seed based, seed = PCC) in a single patient. How can we visualize the map of the (expected) DMN of this single patient in freeview? We tried an overlay with <subjectname>/mri/orig.mgz and <session>/bold/fc.lpccseed.surf.lh/pr001/L_Posteriorcingulate/sig.nii.gz which didn't work. Please help! Best, Martin

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Freesurfer at 7T
by Lucy Hiscox 08 Sep '14

08 Sep '14

Dear Freesurfer experts, I am currently trying to segment a 7T image at 0.8 isotropic resolution. I have an MPRAGE scan and a Gradient echo, and want to coregister the data before processing to correct for inhomogenities, but unsure whether I can use FSL instead of SPM. I am following these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I am new to SP8 and not sure what I would have to do with this information specifically: (i1./i2 .* (i2>20)) .* 100. Also, is it possible to just use the recon-all process or would you recommend going through each step individually outlined above? Is the second option the option for keeping the voxels at 0.8? Furthermore, I read somewhere that you have to use the -cm -aseg command to keep the voxels the same. is this true? Best wishes and many thanks, Lucy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Process with a 0.23T scan
by merlinva2012＠grannet.grm.sld.cu 08 Sep '14

08 Sep '14

Dears experts, I would be very grateful if help me with the following doubts: 1- My data was collected with a 0.23T scan. How i can process it?,Should i make any kind of pre-process before to begin with recon-all? 2- I want only to get the statistics of the caudate nucleus. Is there any way to obtain only this in the segmentation and therefore save time? Thank you. Dr. Merlin Vedecia -- Nunca digas nunca, di mejor: gracias, permiso, disculpe. Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/

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