Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

Extracting LGI values
by Alan Francis 04 Sep '13

04 Sep '13

Hi Marie et al, I have run recon all on the data and calculated LGI for all the brains in my dataset. How does one go about extracting LGI values for each region (eg left Pars Triangularis). Is the Folding index given in the aparc stats sheet the same as LGI? thanks so much, Alan

2 5

Recon checker - actual file order disagrees with common file order
by Sinead Kelly 04 Sep '13

04 Sep '13

Dear all, I have preprocessed my data using Freesurfer v5.2. I have checked the the recon-all.log for each subject to make sure that the process completed without error and that all the appropriate files were created. I have also visually inspected each image. However, when I run recon checker (from freesurfer QA tools) I receive the following error for all of my subjects: 'actual file order disagrees with common file order'. Is this a bug or do I need to re-run the preprocessing again from scratch? If I need to re-run, is there a way to ensure that this won't happen again? Kind regards, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

2 1

Mask from cortical parcellation
by stdp82＠virgilio.it 04 Sep '13

04 Sep '13

Hi list, I need to create a mask of frontal, parietal, temporal and occipital lobes in a subject by using cortical parcellation output. Is it possible? Eventually, how can I transform these masks file to mii.gz (to import them in FSL analysis). Thank you very much. Regards, Stefano

3 2

questions regarding longitudinal processing
by Rongxiang Tang 04 Sep '13

04 Sep '13

Hi All, This may seem to be an easy question, I would just like to confirm... I have two groups that underwent different types of training and were measured at two time points (before and after training). My understanding is that I should use the longitudinal scheme in freesurfer to run recon-all? I have processed all data using normal recon-all command, and was wondering if I should rerun them all with the longitudinal command: recon-all -subjid <tpNid> -all Thanks in advance, Catherine

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nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280)
by Elena Molina 04 Sep '13

04 Sep '13

Hi Freesurfers, I am running recon-all -autorecon1 and I have an error like this: /libdisk/tmp_EMM/subj/mri /libdisk/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux neuron1 3.3.8-gcg-201303011431 #1 SMP Fri Mar 1 14:34:57 PST 2013 x86_64 x86_64 x86_64 GNU/Linux Wed Sep 4 14:45:46 UTC 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.28384 /libdisk/tmp_EMM/subj/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28384/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28384/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=10.02, TE=4.56, TI=600.00, flip angle=12.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.28384/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Sep 4 14:45:49 UTC 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.28384/nu0.mnc ./tmp.mri_nu_correct.mni.28384/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28384/0/ -iterations 1000 -distance 50 [Elena@neuron1:/libdisk/tmp_EMM/subj/mri/] [2013-09-04 14:45:49] running: /libdisk/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.28384/0/ ./tmp.mri_nu_correct.mni.28384/nu0.mnc ./tmp.mri_nu_correct.mni.28384/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /libdisk/freesurfer/mni/bin/sharpen_volume line 153. Processing:.................................................................Done nu_estimate_np_and_em: crashed while running spline_smooth (termination status=11) nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) Does anyone have any idea how I can fix this? Thanks in advance Regards, Elena

1 0

regarding freesurfer
by swathy p.s 04 Sep '13

04 Sep '13

once freesurfer is installed ,how do i run it every time?

2 1

recon-all -aseg.stats doubt
by Anupa AV 04 Sep '13

04 Sep '13

Dear FS experts, I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 for my analysis. After recon-all with hippo-subfield, only 45 brain volumes were genreated in aseg.stats file. Freesurfer v.5.1 analysis were able to generate cortical structure's volumes also. Where v.5.2 mainly generated subcortical volumes like caudate. putamen, amygdala and so on. MAy I knw, is there any way to generate cortical structures also using recon-all command.. Any help 'll be greatly appreciated.

3 3

QDEC for subcortical segmentation
by ye tian 03 Sep '13

03 Sep '13

Dear freesurfers, Is there a way to visualize glm for volume segments in qdec, i.e., instead of analyzing and visualizing vertices on the surface we analyze and visualize voxels on the volume? For example, I would like to ask whether or not regions of posterior/anterior cingulate shrink/expand with age? Thank you very much! Sincerely, Ye

1 0

Qdec: regression with different numbers of variables
by ye tian 03 Sep '13

03 Sep '13

Dear Freesurfers, I am studying cortical thickness as a function of age (continuous) and meditation practice (categorical, level1=Normal, level2=TM). I have three separate cases of qdec, regression1, regression2 and regression3. Regression1: Discrete (Fixed Factor) = meditation; Continuous (Covariate) = age Regression2: Discrete (Fixed Factor) = meditation; Regression3: Discrete (Fixed Factor) = meditation; Nuisance Factor = age For the question "Does the average thickness differ between Normal and TM?", Regression1 and Regression3 have identical result, which is different from Regression2, i.e., (1 = 3 !=2 ). May I infer from this result the following about qdec: 1) Regression1 and Regression3 both fit cortical thickness,y, to the model y = b0 + age*b1 + meditation*b2 + err = y_hat + err Regression2 fits: y = b0 + b2*meditation + err = y_hat + err 2) Some function of y_hat goes into the "average thickness", hence the difference between 2 and the others. However, what role does "Nuisance Factor" play in this case? Thank you very much! Sincerely, Ye

3 8

what is the minimum information needed to create a custom template?
by David Romano 03 Sep '13

03 Sep '13

Hi everyone, If I only have lh.sphere and lh.sulc files for each of collection of subjects, would this be enough information to generate a template for registering further subjects? I was thinking of trying to follow the workflow described on the page: https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates (in the section titled "Creating a registration template from scratch (GW)"), but wasn't sure whether more than just native spherical coordinates and convexity information would be implicitly required by the mris_make_template command. (The "Positional Arguments" table that appears on the page: https://surfer.nmr.mgh.harvard.edu/fswiki/mris_make_template only asks explicitly for references to the hemisphere data for a collection of subjects.) Thanks in advance for you help, David Romano (P.S. There's also appers to be a typo in the "Positional Arguments" table I mentioned above: In the description section for position 2, the {hemi} and {sphere_name} values seem to be reversed.)

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