Freesurfer April 2016

freesurfer@nmr.mgh.harvard.edu

122 participants
173 discussions

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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Calculation of effect sizes
by Jockwitz, Christiane 25 Apr '16

25 Apr '16

Dear FreeSurfer Experts, I've got a question regarding effect sizes: I did a local gyrification analysis using QDEC. I obtained several significant clusters from the analysis for whom I would like to calculate some effect sizes. On the website/helpline, I saw that fscalc might do this job. Therefore, I would need the gamma.mgh file as well as the rstd.mgh file 1. The gamma.mgh is supposed to contain the contrast effect size. What coefficient of determination is that? 2. When the gamma.mgh is divided by the standard deviation (rstd.mgh), I get an output.mgh file, which contains positive as well as negative values ranging from -1 to +1. Since I don't know which coefficient of determination is used in this calculation, I have problem to interpret these values. What value would be a high/low effect size? 3. I would like to calculate this effect size for my significant cluster instead of vertex-wise effect size. I tried to perform this using mri_segstats. Is that right? Thank you very much in advance. Best Christiane

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Intraparietal sulcus - incorrect registrations
by Bastian Cheng 25 Apr '16

25 Apr '16

Dear all, I am creating a hand-drawn label of the Intraparietal sulcus on fsaverge. When I register it to an individual brain (mri_label2label), the area is incorrectly registered and comprises adjacent brain structures that I am not interested in analyzing (specially the neighboring sulci). I know that registration works with my data in general, since other regions (manually drawn on fsaverage, i.e. various pre-motor areas) are correctly registered. is there any bias or "reduced" accuracy when registering regions of interest located at the parietal cortex? I am aware that aparc2009 comprises an area called "S_inrapriet_and_P_trans", but I've found that this label is not restricted to the sulcus (in individual segmentations). Any help would be appreciated! Bastian

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Research Fellow for Pediatric NeuroImaging Genetics and Epigenetics
by Anqi Qiu 25 Apr '16

25 Apr '16

A prospective, longitudinal birth mother-offspring cohort study (Growing Up in Singapore Towards Health Outcomes; GUSTO) study provides a unique opportunity to investigate 1) gene-environment influence on cognitive and brain development; 2) the regulation of epigenetic memory on the development of childrens mental health. GUSTO establishes the intense assessment of cognition, emotional, brain imaging, genetics and epigenetics from infancy onwards and environmental measurements, such as maternal mental health, nutrition, social support etc. This is a longitudinal study that started in 2009. We now have collected infant brain images at multiple time points, cognitive behavior data at multiple time points, genotyping data, and epigenetic data at multiple time points. We are now seeking researchers who are interested in mining GUSTO data at all levels. We aim to identify new markers characterizing environmental, genetic, and cognitive factors and hence explaining epigenetic markers and childrens mental health. The position includes opportunities to apply novel computational models to high-dimensional data sets and develop expertise in 'big data' analysis in neuroscience and to work within a highly multidisciplinary research setting that includes expertise in bioinformatics and biostatistics. Requirements: · PhD on cognitive or neuroscience, neuroimaging, bioinformatics, computer vision, statistics, or relevant field · Experience on mining high dimensional data · Good communication in English language · English writing skill is a must. If you are interested in the jobs listed above, please send your CV to Associate Prof. Anqi QIU Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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lh-Whitesurf
by Hassan bakhshi 25 Apr '16

25 Apr '16

Hello, I couldn't get an answer from you so I will ask my question again: In Freesurfer stats there is a feature named lh-WhiteSurfArea. where is exactly this WhiteSurfArea and how can I show it in freeview on surface or image? Kind Regards, Hassan

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(no subject)
by Николай Семибратов 24 Apr '16

24 Apr '16

Dear experts, I would like to ask you for some advice about matrix. I use FreeSurfer for automatic segmentation of infant brains and have a problem with infants under 6 months. Could you give me advice what are the optimal parameters of the matrix for automatic segmentation from newborns to 6-month-olds? I work on Philips Ingenia 1,5T. T1 3D program runs with the settings ACQ matrix 244x216, TR / TE 7.3 / 3.4. Reconstruction matrix 288, Voxel size 1,05 mm. Any advice would be really appreciated! Best Regards Dr N. Semibratov

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lh-WhiteSurfArea
by Hassan bakhshi 24 Apr '16

24 Apr '16

Hello, In Freesurfer stats there is a feature named lh-WhiteSurfArea. where is exactly this WhiteSurfArea and how can I show it in freeview on surface or image? Kind Regards, Hassan

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Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
by Ramtilak Gattu 24 Apr '16

24 Apr '16

Hello Bruce, Attached are the files for two subjects with brain.mgz and lh.white. https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts… The values of WM in those regions in brain.mgz are above 90. Thanks Regards Tilak ________________________________________ From: Ramtilak Gattu Sent: Saturday, April 23, 2016 5:26 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation 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 misregistration with the atlas if so where can I find the results after the non linear registration and would it be possible to improve with any more expert options during the registration and the segmentation subsequently. 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. > > >

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improving white/grey segmentation in recon -all for better volume estmation
by Ramtilak Gattu 24 Apr '16

24 Apr '16

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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Freesurfer April 2016