Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
by Ramtilak Gattu 30 Mar '16

30 Mar '16

Sorry, Actually just found out that the receiving coil is the 12 channel head coil and the transmitting coil is the body coil. I am attaching a snapshot showing the sag orientation of the three cases that I previously mentioned and uploaded for your review. >From these figures do you really think there is not enough contrast, just wondering 1) why it worked in the bottom image and it failed in the upper two (T1_sag_comparison.jpg) 2) it failed in the left image and did good in the right image (T1_sag_comparison_2.jpg). We have similar data in 25 of the subjects. Is there a way to salvage the existing data and improve our results we will certainly follow your input in changing the existing protocol and collect some data and run the analysis to see if it improves the results. One more thought is if is there any other way around to increase the contrast by taking help from T2 image and run recon-all. Do you think it will help? Thanks for you help . Regards Tilak ________________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: Monday, March 28, 2016 11:22 AM To: Ramtilak Gattu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation what was the transmit coil? I think I would either reduce the voxel sizes a bit or not use grappa. Probably go to 1.2 mm or so, which would be a 70% increase in SNR. That won't help the transmit bias field though if you have one. The 8 channel can also sometimes be a problem. The 32 channel coils work much better On Mon, 28 Mar 2016, Ramtilak Gattu wrote: > Hey Bruce, > > The scans are done on 3T Siemens TRIO and 8 coil head channel with a GRAPPA of 2. > > Here is the screen shot of protocol used. > > https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts… > > Thanks > > Regards > Tilak > > > > ________________________________________ > From: Ramtilak Gattu > Sent: Sunday, March 27, 2016 3:23 PM > To: Bruce Fischl > Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation > > Hey Bruce, > > I have uploaded the files in > > https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts… > > I have also included the 001.mgz in there. > > Thanks > > Regards > Tilak > > ________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Sent: Saturday, March 26, 2016 8:35 PM > To: Ramtilak Gattu > Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation > > can you send me the rawavg.mgz from the subjects's mri file instead of > these dicoms (which I can't read) > On Sat, 26 Mar 2016, Ramtilak Gattu wrote: > >> >> Hey Bruce, >> >> >> Thanks for the quick reply. >> >> >> I have uploaded the cases in >> >> >> https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts… >> xWlpwBQnNAhG8%3d&docid=0a72431d82b4d4b9b924cccbdfb7f34f8 >> >> >> The voxel dimensions are 1x1x1 mm. >> >> >> >> Thanks >> >> >> Regards >> >> Tilak >> >> >> >> ____________________________________________________________________________________________________________________________________________________ >> From: Ramtilak Gattu >> Sent: Friday, March 25, 2016 9:59 PM >> To: freesurfer(a)nmr.mgh.harvard.edu >> Cc: tilakgattu(a)hotmail.com >> Subject: improving white/grey segmentation in recon -all for better volume estmation >> >> Hello all, >> >> >> We have run recon -all on some healthy control subjects T1 images but we found out that the gray-white segmentation on half our subjects is >> bad and it leads to increased white matter volumes and decreased gray matter volumes. I have included a snap shot showing the difference in >> segmentation from bad to good for 3 cases >> >> https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts… >> WPDE1klUw%3d&docid=0dd4546a8004f46578b7a2177b192806a >> >> . The parameter in the sequence are TE=4.92 ms, TR=19 ms, Flip angle =20 degrees. and use a snapshot one slice to show the good CNR. We are using >> Freesurfer version 5.3. >> >> >> Thanks >> >> >> Regards >> >> Tilak. >> >> >> > > > 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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Qdec
by tom parker 30 Mar '16

30 Mar '16

Hi Freesurfers, I compared 2 groups, while controlling for 1 covariate in qdec using freesurfer 5.1. There were no significant interactions with the covariate so I need to use DOSS. I read on several post that DOSS has some bugs related to the generation of contrasts in qdec and that mri_glmfit should be used to run a DOSS analysis. However, when I ran my analysis with DOSS in qdec I saw that the C.mat file looked like this: 1 -1 0, which seems correct to me. My question is can I use DOSS in qdec in this case? Or are there other bugs related to using it in qdec? Thank you so much!

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whole brain is yellow
by Miracle Ozzoude 30 Mar '16

30 Mar '16

Hello Douglas, this was the command i used "Freeview -f $ SUBJECTS_DIR / fsaverage / surf / lh.inflated -viewport 3d Once I opened freesurfer, I viewed lh.secondsessionscore1.glmdir--> cache.the30.pos.sig.cluster.mgh using the overlay icon ; and lh.secondsessioncore1.glmdir ---> cache.the30.pos.sig.ocn.annot using the annotation icon" Thanks

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Increase VBOX disksize
by shi yao wang 30 Mar '16

30 Mar '16

Dear Sir/Madam I am using freesurfer to proceeding brain MRI data. I have 30 cases. However, the space for home is no enough. I am wondering how can I increase disk space to computing my data. I use Vbox unbentu system. thanks Lawrence

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Re: [Freesurfer] Surface area of an fsaverage label
by Jaiashre Sridhar 29 Mar '16

29 Mar '16

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Re: [Freesurfer] Surface area of an fsaverage label
by Jaiashre Sridhar 29 Mar '16

29 Mar '16

Douglas, This is my command line: label_area lh fsaverage lh.temporalpole Output: bash-3.2$ label_area lh fsaverage lh.temporalpole reading /Volumes/project/fsaverage/surf/lh.smoothwm... adjusting for group surface area 1.31 (82220 / 62822) fsaverage: lh.temporalpole - 512.352 square mm Thanks, Jaiashre. Re: [Freesurfer] Surface area of an fsaverage label<https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg46383.html> 2016-03-29<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Douglas N Greve<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> what is your command line? Re: [Freesurfer] Surface area of an fsaverage label<https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg46368.html> 2016-03-28<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Bruce Fischl<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Hi Jaiashre, yes, it should do the correction for average surface area, and should print out a message indicating it is doing so. Something like: adjusting for group surface area ... cheers Bruce [Freesurfer] Surface area of an fsaverage label<https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg46366.html> 2016-03-28<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Jaiashre Sridhar<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Hello, I have used label_area to compute the surface area of a desikan label on fsaverage. Is the correction factor taken into account during computation with this function? Thanks, Jaiashre.

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Surface area of an fsaverage label
by Jaiashre Sridhar 29 Mar '16

29 Mar '16

Hello, I have used label_area to compute the surface area of a desikan label on fsaverage. Is the correction factor taken into account during computation with this function? Thanks, Jaiashre.

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Visualising regional values on the surface
by Kirstie Whitaker 29 Mar '16

29 Mar '16

Hi, I'd like to show correlation coefficients by region on the brain surface. So for example, if I've calculated a modular decomposition in a network analysis for each region of the D-K atlas I'd like to be able to color each atlas region according to the module it has been assigned to. It seems like I have to do something with the ?h.aparc.annot files and a colour lookup table but I'm not sure exactly what. Thank you! Kx -- 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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Cognitive & Brain Sciences PhD opening call, University of Trento, Italy
by Jovicich, Jorge 29 Mar '16

29 Mar '16

Dear All, We are pleased to announce the opening of a call for 14 fellowships for our international PhD Program in Cognitive and Brain Sciences (CIMeC), commencing in November 2016 at the University of Trento, Italy. As you will see from the links below, the PhD call is open to several fields of cognitive neuroscience research. Interested candidates should feel free to contact the PIs that might have topics of interest to them. PhD areas outline: http://web.unitn.it/en/drcimec/37990/32nd-cycle-research-topics-2016-call PhD Application summary: http://web.unitn.it/en/drcimec/10141/application-summary-and-process PhD Application link: https://webapps.unitn.it/Apply/en/Web/Home/dott *PhD Application deadline: Tuesday May 10, 2016, at 4pm ECT* CIMeC: http://web.unitn.it/en/cimec Supplementary information about CIMEC's doctoral program: -CIMeC ranked 1^st in Italy for Quality of Research 2013 <http://www.unitn.it/en/ateneo/1684/anvur-report-2013-trento-is-ranked-first…> -2014-2015 UNITrento ranks 1st in Italy in the rankings of THE - Times Higher Education <http://www.unitn.it/en/ateneo/1636/rankings> -3-yr program: Nov. 1, 2016- Oct. 31, 2019 -Courses are given in English -14 positions, 100% funded -Salary: starting at €1.100/mo., tax-free -Winners receive a €2800 tax-free research/mobility budget -Winners are eligible for a €150/month residential contribution -Why choose UniTrento <http://www.unitn.it/en/ateneo/1629/why-choose-unitrento> - FAQ: http://www.unitn.it/en/drcimec/10142/frequently-asked-questions - More information: phd.cimec(a)unitn.it <mailto:phd.cimec@unitn.it> -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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registering data to template
by Clara Kühn 29 Mar '16

29 Mar '16

Dear FreeSurfer experts, I would like to analyze my longitudinal data also cross-sectionally at single time points. I am a little confused as to how to register my data to the template and smooth it accordingly. Do I have to do it once with a cross-sectional command and once with a longitudinal command? This is what I thought I understood: for LME this registers the data to the template: mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template --hemi lh --meas thickness --out lh.thickness.mg and this smoothes it: recon-all -s name -qcache -target name_of_template In that order? for QDEC (single tp) I use this to register and smooth: long_mris_slopes --qdec ct/qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache kids_template --sd $SUBJECTS_DIR So then, when would I use this?: long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out qdec/cross.qdec.table.dat I am a little confused by the longitudinal option for QDEC when it can't really deal with such data. Should I register and smooth (eg) time point 1 of all my participants to look at it in QDEC as if it were cross-sectional data with this?: mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh And when do I need to use this?: mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target kids_template --hemi lh --meas thickness --out lh.thickness.mgh? The possibilities and the ever so slightly changing commands are somewhat overwhelming, sorry... Thanks in advance, Clara -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse 1A 04103 Leipzig, Germany Phone: +49 341 - 9940 2271 Fax: +49 341 - 9940 2260 Web: www.cbs.mpg.de E-Mail: ckuehn(a)cbs.mpg.de

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Freesurfer March 2016