Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

FLIRT in Han et al., 2006
by Lars M. Rimol 27 Apr '16

27 Apr '16

Hi, I wish to test the reliability of series of three T1 scans that were collected over a period of a few months. The Han et al., 2006 paper recommends using FLIRT to do a linear registration between the scans and then the volumetric registration matrix is applied to the corresponding surfaces (please see quote at the bottom of this e-mail). I was wondering if this is the way to reproduce what was done in that paper: 1) recon-all -all on all three scans 2) register e.g., the 001.mgz from tp2 and tp3 to tp1 using FLIRT; which timepoint was chosen as the reference tp in Han et al.? Or was some type of average template created? Registering all other images to one timepoint seems contrary to the thinking behind the FreeSurfer longitudinal stream (which of course didn't exist at that time). Would you recommend using the FS longitudinal stream in stead? 3) apply the registration matrix to 'h.area and *h.thickness. Here the question is how do I apply the registration matrix to the area and thickness files? I saw mris_apply_reg was recommended in order to register to xhemi.rh.w-g.pct.mgh but I'm not sure if I can use mris_apply_reg here? from the 2006 paper: "[..] a simpler linear registration is adopted to perform the intrasubject surface alignment, and surface point correspondence is then built according to their Euclidean distance in the registered space [..]. The linear registration is computed using the FLIRT linear registration tool (Jenkinson et al., 2002). The volumetric registration matrix is then applied to the corresponding surfaces." Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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labels
by Trisanna Sprung-Much 27 Apr '16

27 Apr '16

Hi there I have two questions regarding using the labels with tksurfer: 1. What exactly has been done to change the .label (e.g. lh BA44.label) to .thresh.label (e.g. lh BA44.thresh.label? 2. The instructions on this page https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps to overlay the labels and set the Min and Max do not seem to work for me - I cannot seem to alter the Min from 2 and the Max from 5. Any thoughts as to why? thanks very much! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Preprocessing functional MRI
by Martin Juneja 27 Apr '16

27 Apr '16

Hello everyone, I am following this page to process fMRI data: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… I am able to run until step-3 but at step 4, I am not sure what should be directory to run this command. If I run the command in SUBJECTS_DIR directory, it runs for a second and creates a mean*.config file. But next step 5 requires *.config file to run, not the mean*.config Just a quick background: I preprocessed all subjects structural data using recon-all and the processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder after preprocessing functional data (after running step-3) is also in SUBJECTS_DIR path. Any help would be greatly appreciated. MJ

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How to post questions in the freesurfer forum
by WENJunhao 27 Apr '16

27 Apr '16

Hello:I want to know how I can post a question in the tutorial of freesurfer in the freesurfer forum and i did what the wiki pages told me to do, and subscribe the mailing list, but i dont get it how to do it, look forward to hearing from you Junhao WEN Institut du Cerveau et de la Moelle épinière - ICM CNRS UMR 7225 - Inserm U 1127 - UPMC-P6 Équipe ARAMIS / Projet CLINICA Hôpital de la Pitié-Salpêtrière - 47, boulevard de l'Hôpital – 75013 Paris Tél:+ 33 (0)1 57 27 40 00

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Re: [Freesurfer] white surf area
by Hassan bakhshi 26 Apr '16

26 Apr '16

Hello Bruce, Sorry I'm in a hurry and its 3rd time I emailed. What is exactly the feature white surface area and how can I visualize it? Kind regards,

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hippocampal subfield analysis - registered two scans prior to analysis
by Lara Foland-Ross 26 Apr '16

26 Apr '16

Hello, I'm beginning a hippocampal subfield analysis in the beta version of Freesurfer 6.0. I have a whole brain T1-weighted image as well as a high-resolution T2-weighted image of the hippocampus. The T2 weighted image covers the entire hippocampus, but not the whole brain. My understanding (and please correct me if I'm wrong) is that I should first run recon-all on the T1-weighted brain, then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag, but that I must first make sure that the two scans are roughly aligned. I was able to successfully register the T1-weighted scan to the T2-weighted scan using mri_robust_register using the following commands: mri_robust_register --mov wholebrain.mgz --dst hippocampus.mgz --cost nmi --lta wholebrain_to_hippocampus.lta -satit --noinit --nosym mri_convert -at wholebrain_to_hippocampus.lta -rl hippocampus.mgz wholebrain.mgz wholebrain_reg_to_hipppcampus.mgz My plan was then to run recon-all on the newly upsampled, registered wholebrain_reg_to_hippocampus.mgz image. And then run recon-all on the T2-weighted scan using the -hippocampal-subfields-T1T2 flag. However, the resampled whole brain T1-weighted image now has only a partial FOV. Is there a way that I can preserve the full field of view in the T1-weighted scan? I've experimented with mri_coreg and flirt and am at a loss. Many thanks in advance, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
by Ramtilak Gattu 26 Apr '16

26 Apr '16

Hello Bruce, Thanks for the response. I previously mentioned the parameters in the earlier discussion for the same topic and you have suggested to decrease the TE and increase the voxelsize to 1.2mm for better SNR. For the recollection I am again mentioning the complete parameters here- The parameter in the sequence are TE=4.92 ms, TR=19 ms, Flip angle =20 degrees, voxel size 1x1x1, receiving coil is the 12 channel head coil and the transmitting coil is the body coil and GRAPPA of 2. We are using Freesurfer version 5.3. I am including all the recon result files for one case for your review. https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts… Thanks Regards Tilak On Sun, Apr 24, 2016 at 1:52 PM, Ramtilak Gattu <tilak(a)neurologicstudies.com > wrote: > Hello Bruce, > > Attached are the files for two subjects with brain.mgz and lh.white. > > The values of WM in those regions in brain.mgz are above 90. > > Thanks > > Regards > Tilak > > > On Sun, Apr 24, 2016 at 1:49 PM, Ramtilak Gattu < > tilak(a)neurologicstudies.com> wrote: > >> >> >> On Sat, Apr 23, 2016 at 7:47 PM, Ramtilak Gattu < >> tilak(a)neurologicstudies.com> wrote: >> >>> Hello Bruce, >>> >>> Thanks a lot for your earlier expert option suggestion in improving the >>> segmentation during the recon process. I am attaching a snap shot where >>> yellow is with expert options and red is with default options. My concern >>> is where I have indicated with blue arrows . Could you please suggest why >>> is it still failing to pick up those areas. Is it because of >>> >>> a) misregistration with the atlas >>> (i) if so where can I find the results after the non linear >>> registration and >>> (ii) would it be possible to improve with any more expert >>> options during the registration and the segmentation subsequently. >>> >>> b) or is it should be just changing the lower limit values for the WM >>> and higher limit values for the GM. I am not sure which way to tune the >>> values should I go low on WM values and go high on GM values. These are the >>> actual values >>> >>> mri_segment -wlo 87.7 -ghi 103.3 >>> mris_make_surfaces -min_gray_at_white_border 79.4 -max_border_white >>> 109.3 -min_border_white 90 -max_csf 68.7 -max_gray 98.7 >>> -max_gray_at_csf_border 84.7 -min_gray_at_csf_border 58.1 >>> >>> For example Should these be changed to >>> >>> mri_segment -wlo 80 -ghi 110 >>> >>> Thanks for your help in advance. >>> >>> Regards >>> Tilak >>> >>> >>> Thanks >>> >>> Regards >>> Tilak >>> >>> ________________________________________ >>> From: Ramtilak Gattu >>> Sent: Wednesday, March 30, 2016 4:26 PM >>> To: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] improving white/grey segmentation in recon >>> -all for better volume estmation >>> >>> Thank you for recommending the expert options. I have run this on two >>> subjects (rows) and you can see the post analysis results on the right >>> (column) in the attached image . As you have mentioned it didnt work well >>> in the cerebellum any other ways to improve in the inferior regions? >>> >>> Thanks >>> >>> Regards >>> Tilak >>> ________________________________________ >>> From: Ramtilak Gattu >>> Sent: Monday, March 28, 2016 5:12 PM >>> To: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] improving white/grey segmentation in recon >>> -all for better volume estmation >>> >>> Thank you, >>> >>> Attached is the scripts folder for one subject . >>> >>> Thanks >>> >>> Regards >>> Tilak >>> ________________________________________ >>> From: Ramtilak Gattu >>> Sent: Monday, March 28, 2016 4:11 PM >>> To: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] improving white/grey segmentation in recon >>> -all for better volume estmation >>> >>> 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. >>> > >>> > >>> > >>> >>> >> > -- ***NOTICE*** The documents accompanying this email transmission contain confidential information belonging to the sender, which is legally privileged. The information is intended only for the use of the individual(s) or entity(ies) named above. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or the taking of any action in reliance on the contents of this emailed information is strictly prohibited. If you have received this email in error, please immediately notify us by telephone at 248-277-3334 to arrange for return of the original documents to us. Thank you.

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coordinates to values
by prasser 26 Apr '16

26 Apr '16

Hi, Could you please let me know the command that takes say, ras coordinates (or a list of them) and a .mgz as input, and outputs the corresponding voxel values from the .mgz? Thanks.

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Ventricular volume
by Anna Harris 25 Apr '16

25 Apr '16

Hi, I'm writing from UChicago to inquire as to what the easiest way to calculate ventricular volumes is using the segmentation tools. I'm having a hard time navigating your wiki. If there is a command line protocol for this listed, can you please refer me to it? Otherwise I may need help walking through the steps, as I've just recently been trained on SPM. I'm also not sure whether if the MRI images I have collected are already standardized, if I need to re-preprocess them in Freesurfer to be able to use the segmentation tools properly. Please advise! Many thanks, Anna

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Two Different T1 Acquisition Planes as recon-all Inputs
by Douglas Merkitch 25 Apr '16

25 Apr '16

Hello Freesurfer experts, We currently acquire two sagittal T1s (136 slices) in our protocol so that we can take advantage of freesurfer's motion correction algorithm; however, we would like to add a coronal T1 (196 slices). In order to cut down on scan time, we are also considering dropping one of the the sagittal T1s and using one sagittal and one coronal T1 as inputs for freesurfer recon-all. When I specified these sagittal and coronal inputs for the recon-all for our test subject, we received the "ERROR: inputs have mismatched dimensions!" My main questions are the following: If we do cut one of the sagittal T1 scans, 1) Would it be possible to use one sagittal and one coronal T1 as inputs? The sequences are identical except for the acquisition plane and number of slices. 2) If it is possible (perhaps by registering with mri_robust_register), what would be the correct procedure for matching the dimensions of these two scans? 3) Are there any other considerations or possible problems with this and does this approach have merit (i.e. would it be advisable to just use one T1 input instead of two T1 inputs that have different acquisition planes)? Any insight would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

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