Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

tksurfer scale bar
by Michael Asghar 01 Apr '16

01 Apr '16

Hi Freesurfer I'm struggling with trying to edit the scale bar in tksurfer. Commands like 'set scalebar_bright 240' work, but draw_scalebar gives an invalid command error. I've tried redrawing, but it doesn't help. Basically, I want the black background to become white (can do it via convert -fill white -opaque black input.tiff output.tiff), but the numbers on the scalebar are invisible now - I need the scale bar text to be black. Also, I get two bits to my scalebar, e.g. negative values at the bottom from -5 to -3, then a grey gap and then positive 3 to 5 in hot colours. How do I get just the positive T values in a suitable distance (they are currently squeezed up at either side). Thanks! Michael This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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bbregister problems with PET data
by Adam Martersteck 31 Mar '16

31 Mar '16

Hi Freesurfer team, I’m encountering a problem using bbregister on PET data: -- When I attempt to register a PET volume to T1-space the asymmetric tracer uptake of the PET throws off proper registration. (Treating the PET as a T1 because of the non-specific white matter uptake > grey matter signal). -- You can really see the bbregister mis-registration in this gif here: https://goo.gl/iM6yrT -- It (expectedly) attempts to find the best match between signal intensities on both the left and right surfaces, but is inherently biased by the asymmetric uptake shifts the entire volume to the right. -- Are there any suggestions for dealing with asymmetric scans like this? Stick with just a simple FLIRT? It doesn't seem to do that great a job for everyone. Cutting left and right hemispheres apart and register separately? Using Martin’s new robust register for multi-modal data? Any suggestions on the parameters of ROBENT? Thanks, Adam

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ERROR running mkcontrast
by Joseph Dien 31 Mar '16

31 Mar '16

Hi, I ran into an odd problem which I was able to fix but wanted to let others know about. This is OS X 10.11.4 with Matlab 2016a and FreeSurfer 5.3. I got the following error when I ran mkcontrast using batch files that previously worked fine: /private/var/folders/wt/vj5q34fs20x50sh_6rcrtkn80000gn/T/Cleanup At Startup/sh.h4SI0w: No such file or directory. ERROR running mkcontrast Looking into the directories in question, I found that while there was no directory named 'Cleanup At Startup’ inside the T directory, there was such a directory inside ‘vj5q34fs20x50sh_6rcrtkn80000gn’. I’m guessing some version update changed the location of this directory. I went into T and performed the following command: mkdir 'Cleanup At Startup' after doing so, everything worked again. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, PhD Senior Research Scientist Maryland Neuroimaging Center University of Maryland, College Park E-mail: jdien07(a)mac.com Cell Phone: 202-297-8117 http://joedien.com

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Surface-based PET maps
by Alshikho, Mohamad J. 31 Mar '16

31 Mar '16

Hi Doug, In order to run surface based analysis on PET maps, I used the following steps: 1. Co-registering SUVR to T1 bbregister --s name --mov suvr.nii --bold --init-fsl --reg reg.dat --o suvr_T1.mgh 2. Concatenate SUVR maps mris_preproc --target fsaverage --hemi lh --iv subject1/suvr/suvr_T1.mgh subject1/suvr/reg.dat --iv subject2/suvr/suvr_T1.mgh subject2/suvr/reg.dat --iv ... --projfrac 0.5 --out lh.suvr.mgh 3. Smoothing(sm) mri_surf2surf --hemi lh --s fsaverage --fwhm 10 --cortex --sval lh.suvr.mgh --tval lh.suvr.sm10.mgh 4.Group analysis (GLM) mri_glmfit--y lh.suvr.sm10.mgh --fsgd fsgd.txt --C X.mtx --surf fsaverage lh --cortex --glmdir lh.suvr 5. Correction for multiple comparisons ( Cluster -wise) mri_glmfit-sim --glmdir lh.suvr --cache 1.3 neg --cwp 0.05 --2spaces # Cache 1.3 ( P<0.05) * In a second analysis for the same set of data, I replaced the first step ( co registration) by the following command line: spmregister --s name --mov suvr.nii --reg reg.dat --o suvr_T1.mgh I got the results as attached ( figure1 using bbregister and figure 2 using SPM register) Kindly, 1. Where this difference came from? In other words, should I expect such like difference between "bbregister" and "spmregister" ? 2. For co registration which command do you recommend "bbregister" or "spmregister" ? Best, Mohamad

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Fwd: 5 year Post Doctoral Fellowship in South Korea - Korean Genome and Epidemiology Study
by Douglas N Greve 31 Mar '16

31 Mar '16

FYI -------- Original message -------- From: "Thomas,Robert" <rthomas1(a)bidmc.harvard.edu> Date: 03/30/2016 5:52 AM (GMT+05:30) To: all(a)nmr.mgh.harvard.edu Cc: Chol Shin <chol-shin(a)hanmail.net> Subject: 5 year Post Doctoral Fellowship in South Korea - Korean Genome and Epidemiology Study A 5-year Post-Doctoral Fellowship is available in South Korea, at the Korean Genome and Epidemiology Study, with the center at Ansan Hospital, about 45 minutes outside Seoul. Those with a PhD is the general area of neuroimaging are encouraged to apply. The support is US $ 70,000/ year, with direct additional support for accommodation. The program is funded by the Korean Government. Agreeing to the full 5 years is necessary, no partial support is possible. The KoGES has been in existence since 2001, and has biannual health exams. Rich demographic and cardiovascular information is collected, GWAS is available. Brain MRI (structural, DTI), sleep (including polysomnography) and detailed cognition evaluations were initiated in 2008, and is now in the second cycle. The Fellowship will focus on the brain-sleep-heart interface, a major role for the Fellow will be oversight and aiding the analysis of MRI data, currently obtained at 1.5 T but to move to 3T during the course of the award. High productivity will be expected, and evidence of prior first author publications will be desirable. The awardee will also work with investigators from Harvard (MGH Martinos Center, Beth Israel Deaconess Medical Center) and Boston University-Framingham Heart Study, and can be expected to have substantial freedom to pursue cutting edge analysis techniques in the neuroimaging and Big Data / “omics” realm. Decisions will be made by the end of April. Prospective candidates will need to travel to Seoul for a meeting with Dr. Chol Shin, the Principal Investigator of KoGES, in April; travel costs are covered. Interested individuals should send their NIH style biosketch to Chol Shin, M.D. chol-shin(a)hanmail.net <mailto:chol-shin@hanmail.net> and Robert Thomas, M.D. rthomas1(a)bidmc.harvard.edu <mailto:rthomas1@bidmc.harvard.edu> ------------------------------------------------------------------------ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Re: [Freesurfer] DODS vs DOSS for correlation analysis
by Cassandra Wannan 31 Mar '16

31 Mar '16

Hi Doug, I'm using version 5.3. I had read about the bug but the release notes for 5.3 didn't mention not using DOSS in Qdec, so I thought the issue must have been resolved. If not, I'll let my colleagues know as I believe some of them are still using DOSS in Qdec. Cheers, Cassie

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Summer School course 'Genetics for Imagers', 8 August - 12 August in Nijmegen, The Netherlands
by Marten.Onnink＠radboudumc.nl 31 Mar '16

31 Mar '16

Dear Freesurfer users, I would like to promote our Radboud Summer School in Nijmegen (The Netherlands) which might be interesting for FSL imaging people that would like to expand their knowledge in the genetics area. This intensive one-week (8 August - 12 August 2016) course covers various aspects of genetics analyses of neuroimaging data. More info here: http://www.ru.nl/radboudsummerschool/courses/brain-behaviour/vm-more-course… Cheers! Marten Marten Onnink, Msc Radboud University Medical Center Nijmegen Department of Human Genetics (855) | PO Box 9101 | 6500 HB Nijmegen | The Netherlands T +3124 36 10981| Email: Marten.Onnink(a)radboudumc.nl<mailto:Marten.Onnink@radboudumc.nl> Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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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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