Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Smoothing at FWHM (Qdec)
by Martin Juneja 16 Mar '16

16 Mar '16

Hello everyone, I am very new to FreeSurfer. Although I know what smoothing means etc. but I am not sure what smoothing level is the best to choose while comparing cortical thinning for patients vs. controls. Qdec gives several options to choose from among 0, 5, 10, 15, 20 and 25. Literature says 10 mm is the typical value to choose but when I calculate clusters, I don't see any significant clusters (at FDR p < 0.05) but at smoothing level 20 mm, I can see several clusters at the same threshold i.e. at FDR p < 0.05. I would really appreciate if someone, expert in this field could guide me regarding this. Also, may be if someone could recommend me a few papers from literature discussing this issue e.g. effect of smoothing on cortical thickness etc., that would be very useful. Thanks, MJ

2 1

mri_fwhm
by John Anderson 16 Mar '16

16 Mar '16

1 0

Problems with file un qdec analysis
by Lisa Delalande 16 Mar '16

16 Mar '16

Hello everyone, I've got some problems with qdec. I have .levels with more than 2 factors. For example a "grpe.levels" with three factors : children (enfant), adults (adultes) and nothing (rien). But if I want to exclude some subjects like children qdec doesn't work anymore (attachment : error message). Is that possible a .levels can not have more than two factors ? Or the problem came from anything else ? Thanks in advance for your help ! Best regards, Lisa

2 2

Anterior to Posterior Length
by Heather Acuff 16 Mar '16

16 Mar '16

Good morning, I apologize if this email was sent out twice. I would like to use anterior to posterior length as a covariate in my DTI analysis. Is there an easy way to obtain this information for each subject? Thank you, Heather

2 5

Regarding: running lgi with freesurfer dev6 and matlab2016a
by Dr Sampada Sinha 16 Mar '16

16 Mar '16

Dear freesurfer expert Marie, I am trying to run lgi after doing recon-all. I am getting stuck with an error. Just wanted to know if freesurfer dev6 is compatible with newest Malta 2016a version. Thanks and regards, Sampada Predoctoral student KGMU, Lucknow India -- Sampada Sinha

1 1

Skull strip
by ulrike kaunzner 16 Mar '16

16 Mar '16

Hi, We have problems with the skull of one subjects (please see below). We tried adjusting the watershed parameters, but it still did not work. What else can we do to change the surface? Thank you for your help! Best, Uli

2 1

error while running dt-recon all
by Jasmin Alves 16 Mar '16

16 Mar '16

Dear Freesurfer experts, FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 I received the following error while running the dt_recon --i 00010001 --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40. The participant is 40. And I received the following error: WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I did notice on previous threads this is a common error that occurs, but the files I have were directly exported from our siemens scanner via Osirix. I also tried running dt_recon using nifti format but that resulted in an error as well. Is there anything else I can do? Thanks, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

3 12

error - mri_nu_correct.mni
by Flavia Niccolini new 16 Mar '16

16 Mar '16

Hello, I was wondering whether you could help with this error: #-------------------------------------------- #@# MotionCor Thu Mar 3 11:35:51 GMT 2016 Found 1 runs /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1 mri_convert /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz --conform mri_convert /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (-0, -0, 1) Original Data has (1, 1, 1) mm size and (160, 240, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz... mri_add_xform_to_header -c /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/transforms/talairach.xfm /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 3 11:35:59 GMT 2016 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux nig05.nig.ioppn.kcl.ac.uk 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PD1 exited with ERRORS at Thu Mar 3 11:36:02 GMT 2016 Many Thanks With Best Wishes Flavia

2 4

aparc stats volume outputting area instead
by Clare Loane 16 Mar '16

16 Mar '16

Hi, I am trying to pull out the volumes from the aparc stats file but when I input the following (below) it produces a file identical to the area instead: aparcstats2table --subjects 001 002 003 --hemi rh --meas volume --tablefile aparc_stats_volume_rh.txt It works fine for thickness and area as well aseg_stats. I would appreciate any help with this. Thank you! Clare

3 4

tksurfer
by John Anderson 16 Mar '16

16 Mar '16

3 4

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Freesurfer March 2016