Freesurfer

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30084 discussions

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

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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

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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

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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

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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

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tksurfer
by John Anderson 16 Mar '16

16 Mar '16

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Postdoc job: Neuroimaging of mood disorders in adolescence at University of Cambridge
by Kirstie Whitaker 16 Mar '16

16 Mar '16

Dear FSL, Freesurfer and Neuroimaging in Python list members (with apologies for cross posting), The closing date for this position is this SUNDAY 20th MARCH, so you don't have much time (although we only need a cover letter and CV type details for your application), but I've been asked to reach out to you because we'd really like to hire the very best postdoc for this role at the University of Cambridge. Please share this email widely with your personal and professional networks. The successful applicant will join a multidisciplinary team of scientists investigating the neural basis and cognitive correlates of behavioural phenotypes in large existing and still being collected longitudinal community and clinical cohorts of adolescents and young adults as part of the Neuroscience in Psychiatry Network (http://nspn.org.uk) Applicants will have a PhD and some postdoctoral experience reflecting an expert level of knowledge in cognitive and behavioural neuroscience together with a working knowledge and interest in longitudinal data analysis and mental illness. The full job advert and instructions on how to apply are at http://www.jobs.cam.ac.uk/job/9696. The role comes with an invitation to interview for a fellowship at Peterhouse, the oldest remaining college in Cambridge. The start date is (reasonably) flexible but projected for May 2016. The funds for this post are available until 31 March 2018 in the first instance. The Clinical School at the University of Cambridge is a proud holder of an Athena SWAN Silver award <http://athena-swan.medschl.cam.ac.uk/> and candidates from groups that are under-represented in senior STEMM positions (such as women and people of colour) are particularly encouraged to apply. If you have any informal questions about this vacancy please contact Professor Ian Goodyer (ig104(a)cam.ac.uk) For information on the application process for this vacancy, please contact Dominic Drane, HR Administrator via email on hradminpsychiatry(a)medschl.cam.ac.uk. Please quote reference RN08523 on your application and in any correspondence about this vacancy. Thank you Kirstie Whitaker -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* www.kirstiewhitaker.com

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Re: [Freesurfer] Editing Lesions in FreeSurfer 5.1
by Allison Rainford 15 Mar '16

15 Mar '16

Hi Bruce, I?ve attached a screen shot of a temporal pole of one of the brains that we have had issues with. Here the issue is that there is a lesion without a very clear boundary for the white matter and freesurfer was unresponsive to simply using white matter edits (placing 255s on the wm.mgz), and so we tried placing control points where we think the white matter boundary should lie. However, we know that control points should not be placed in these dark spots of a lesion. Thank you, Allison

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Recon Reprocessing Issues
by Champe Barton 15 Mar '16

15 Mar '16

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Cortical thickness analysis -- Qdec
by Alshikho, Mohamad J. 15 Mar '16

15 Mar '16

Hi Doug, I have two groups of subjects and I want to study the difference in cortical thickness between the groups. I used Qdec to run the analysis and I got significant difference between the groups in areas support what I am looking for. I repeated the analysis as mentioned in Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 1. My data is previously cached so I ran the command : mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh 2. GLM analysis: mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir 3. Correction for multiple comparison mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces Surprisingly, the results are totally different from what I get in Qdec. I checked Qdec's commands generated in Terminal and I noticed that it uses the command "mri_surfcluster" instead of " mri_glmfit-sim " Kindly, 1. What is the difference between "mri_surfcluster" and " mri_glmfit-sim " 2. Is it expected that we get different results as an output of the previous two different methods 3. In order to run statistical analysis regarding volumetrics and cortical thickness. Which method is more advisable, Qdec or the previous command lines (1-3) Best, Mohamad

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