Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Question regarding control points
by Martijn Steenwijk 12 Mar '12

12 Mar '12

Dear all, I've been correcting a recon with controlpoints and correction of the skull strip. Although the result is a lot better, still a part of the temporal lobe is missed, although I have been putting control points in this area. Is there a way to improve this? See attached image (left: pre-correction, right: post-correction). Best, Martijn

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[freesurfer] Is there any way to get the image from Tksurfer with white background?
by zhang mingxia 12 Mar '12

12 Mar '12

Hi dear freesurfer experts, I am making pictures for publication. The images saving from Tksurfer are black backgrounds. Is there any way to save the image with white background? Thank you very much Mingxia Zhang

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mri_glmfit -sim processing time?
by Juke Cha 12 Mar '12

12 Mar '12

Hi all, I'm running a simulation to get corrected p values. I set the iteration as 5000 times and it's a group analysis of ~40 subjects. Now the simulation has been going for three days on 2.8 Hz i7 CPUs and not done yet. Simulation on 100 iterations completed pretty quick so assumed a couple of days would be enough. Is this supposed to be this long? Is there any way to check if something goes wrong? Best, Juke -- Juke Cha, M.S. Ph.D Candidate, Program in Neuroscience Laboratory for Computational Neurodiagnostics (LCN)<http://www.lcneuro.org/> Dept of Biomedical Engineering Stony Brook University School of Medicine email: cha(a)lcneuro.org office: 631-632-1992 fax: 631-632-3222

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question about fcfast
by yingtan＠nmr.mgh.harvard.edu 12 Mar '12

12 Mar '12

Hello, everyone, I have question about fcfast. we have several bold numbers and run fcfast at the same time. For example, fcfast -id 070324_4TT00201 -mpr 3 -bold 15,16 -roi /ncf/tools/mtt24/seeds/N12Trio_avg152T1_reg6mm_40_-18_48.nii.gz I don't know if the final correlation (Z) images are mean value when fcfast completes the fcMRI anaysis. Thanks in advance. Best, Ying Tan

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dt_recon with siemens skyra data
by John Fredy 12 Mar '12

12 Mar '12

Hello all, I am trying to process siemen dti data from a skyra model in the dt_recon software. But the software fails in the conversion from Dicom. Anyone had experience with the DTI sequence from a skyra model? Any suggestion is welcome Thanks in advance John Ochoa Bioingeniería Universidad de Antioquia

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White matter intensity normalisation
by Charlotte Bernard 12 Mar '12

12 Mar '12

Dear Freesurfer users, I run FS on my 670 subjects. All the scans were acquired on a 1.5T Philips scan. I noticed that my values in the WM are near 100-110 but not exactly 110. I think it is a problem! Is it link to the 1.5T? How can I fix it? I joined my log file of QA tools: could you help me to undertand the output? wm-anat-snr results: SNR: Anatomical signal-to-noise ratio in white matter mWM: Mean white matter intensity value stdWM: Standard deviation of white matter intensity value voxWM: Total number of white matter voxels in eroded mask SubjID SNR mWM stdWM voxWM 1 13,37* 104,18 7,79* 24181 <------ 2 14,79* 105,90 7,16* 22148 <------ 3 13,57* 104,75 7,72* 37341 <------ 4 12,67* 104,18 8,22* 29311 <------ 5 14,36* 105,44 7,34* 48083 <------ 6 11,40* 103,92 9,11* 47704 <------ 7 14,52* 104,71 7,21* 25706 <------ 8 9,92 101,42 10,22 40187 9 11,31* 104,28 9,22* 22967 <------ 10 11,61* 102,92 8,86* 19850 <------ 11 14,78* 105,05 7,11* 26607 <------ 12 11,36* 105,33 9,27* 15465 <------ 13 11,30* 103,69 9,18* 34685 <------ 14 11,73* 105,20 8,97* 40471 <------ 15 11,92* 104,04 8,73* 13777 <------ 16 9,46 102,04 10,79 30314 17 12,60* 106,40 8,44* 38432 <------ I thought it can help me to quickly identify the subjects who didn't work for this step. For example, the subject n°8 has a problem? Thanks, Charlotte

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Buckner Tutorial data set
by Ahmed, F, Me <fahmed＠sun.ac.za> 12 Mar '12

12 Mar '12

Hello Freesurfer experts, I'm trying to extract the data from the tutorial dataset "buckner_data-tutorial_subjs.tar.gz" by typing this command "tar -xvzf buckner_data-tutorial_subjs.tar.gz" and after it finished, I got this error message: tar: buckner_data/tutorial_subjs/130: Cannot create symlink to `group_analysis_tutorial/130': Operation not supported buckner_data/buckner_public_distribution.README.txt tar: buckner_data/tutorial_subjs/fbert-feat/fbert.gfeat/.files: Directory renamed before its status could be extracted tar: buckner_data/tutorial_subjs/fbert-feat/fbert1.feat/.files: Directory renamed before its status could be extracted tar: buckner_data/tutorial_subjs/fbert-feat/fbert2.feat/.files: Directory renamed before its status could be extracted tar: Error exit delayed from previous errors [root@localhost EONCS]# Can someone please explain to me why this happened and what I can do to fix this? Thank you and Kind Regards, Fatima ________________________________ E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail.

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aseg.mgz doe not look as good after Longitudinal Processing on 5.1
by Brain Apprentice 12 Mar '12

12 Mar '12

Hi Surfers, I have done some Longitudinal Processing on a bunch of subjects and although the pial and white surfaces are looking good for the most part, the aseg segmentation are often looking much much worse. I have attached a sample screen grab to show you what I mean. The images on top are of the Longitudinal Processed axial and sagittal views. The images on bottom are of the same subject before the Longitudinal Processing has occurred. It is possible I am doing something wrong. I just thought I would throw it out to the experts to see if they are having similar experiences. Thanks very much, B.A.

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read and write thickness file ?
by tulu＠ms36.hinet.net 11 Mar '12

11 Mar '12

Dear FS experts, I would like to read cortical thickness data from lh.thickness.fwhm10.fsaverage.mgh file and do some calculation. then save the result as thickness file. which matlab script should I use ? sincerely yours Jung-Lung, Hsu

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Re: [Freesurfer] How to access information in gamma.mgh and gammavar.mgh?
by Douglas Greve 11 Mar '12

11 Mar '12

It's a "volume" files with about 160000 values. If you know which vertex you want, you can load it into matlab with MRIread.m On 3/11/12 1:44 PM, Knut J Bjuland wrote: > Hi Doug > > Could you please explain how I can extract the standard deviation in > > rstd.mgh? Should I use mri_info or matlab? > > Knut J > > > > On 10. mars 2012 23:17, Douglas Greve wrote: >> Hi Knut, you will need the effect size which is gamma/rstd where rstd is >> the the standard deviation of the noise which is stored in rstd.mgh in >> the glm directory. >> doug >> >> On 3/10/12 10:35 AM, Knut J Bjuland wrote: >>> Dear Sirs/Madams >>> >>> How to access information in gamma.mgh and gammavar.mgh? Which command >>> should I use? Since it not explained in the tutorial. I want to use it >>> to calculate effective population size? How large population size is >>> needed to demonstrate a deviation between to population in cortical >>> thickness? >>> >>> Best regards >>> >>> Knut J >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> >> > >

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Freesurfer March 2012