Re: [Freesurfer] Hippocampal subfield segmentation with T1 and T2
Hi Cassie, It seems to be a problem with mri_robust_register, when trying to allíen the t1 and t2 scans. Martin, any ideas? Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Cassandra Wannan <cwan...@student.unimelb.edu.au> Sent: Thursday, January 18, 2018 10:59:45 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal subfield segmentation with T1 and T2 Hi all, I've been trying to run the hippocampal subfield segmentation with T1 and T2 images, and haven't had much luck. I had previously run recon-all on all my scans in v5.3, but testing on one subject I re-ran recon-all with the additional T2 scan, and that seems to have run fine. However, when I try to run the subfield segmentation, I am getting errors. My command line is: recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/T2.mgz CRC040T1T2 -no-isrunning but I have also tried: recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/orig/T2raw.mgz CRC040T1T2 -no-isrunning and: recon-all -s CRC040 -hippocampal-subfields-T1T2 ./CRC040.nii CRC040T1T2 -no-isrunning The error I am getting is: /Applications/freesurfer_v6/bin//mri_robust_register --mov /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/norm.mgz --maskmov /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//wholeBrainMask.mgz --dst /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/T2.mgz --lta /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta gunzip: can't stat: /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz (/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 192) MATLAB:badSwitchExpression Any idea what could be causing the issue? The hippocampal pipeline runs fine without the T2 scan, however I am planning to use the subfield segmentation as a mask for some white matter tractography analysis in FSL, and the dimensions of the output are not close to my nifti files. I was hoping that using the T2 registration would help with this, but can't get it to work! Any help would be greatly appreciated. Kind regards, Cassie ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] Hippocampal subfield segmentation with T1 and T2
Hi all, I've been trying to run the hippocampal subfield segmentation with T1 and T2 images, and haven't had much luck. I had previously run recon-all on all my scans in v5.3, but testing on one subject I re-ran recon-all with the additional T2 scan, and that seems to have run fine. However, when I try to run the subfield segmentation, I am getting errors. My command line is: recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/T2.mgz CRC040T1T2 -no-isrunning but I have also tried: recon-all -s CRC040 -hippocampal-subfields-T1T2 CRC040/mri/orig/T2raw.mgz CRC040T1T2 -no-isrunning and: recon-all -s CRC040 -hippocampal-subfields-T1T2 ./CRC040.nii CRC040T1T2 -no-isrunning The error I am getting is: /Applications/freesurfer_v6/bin//mri_robust_register --mov /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/norm.mgz --maskmov /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//wholeBrainMask.mgz --dst /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/T2.mgz --lta /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta --noinit --cost NMI -nosym >/dev/null: Signal 127 ERROR: cannot find transform file /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/mri/transforms/T1_to_CRC040T1T2.v10.lta gunzip: can't stat: /data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz (/data/blinky/work/cassie/CRC/crcimage/sam_mprage/CRC040/tmp/hippoSF_T1T2_v10_CRC040T1T2_right//T2resampledLikeT1.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 192) MATLAB:badSwitchExpression Any idea what could be causing the issue? The hippocampal pipeline runs fine without the T2 scan, however I am planning to use the subfield segmentation as a mask for some white matter tractography analysis in FSL, and the dimensions of the output are not close to my nifti files. I was hoping that using the T2 registration would help with this, but can't get it to work! Any help would be greatly appreciated. Kind regards, Cassie ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Hippocampal subfield segmentation with T1
Hi Xiaowei, this was my mistake when I wrote the article in the wiki. The images do not need to be in the same orientation (I already changed this in the wiki). They need to be coarsely registered in physical coordinates (i.e., the need to look approximately registered when you open them in FreeView). If you manually rotate / translate the T2, make sure that you check the "do not resample" box when you save the rotated scan in order not to lose information. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> To: "Xiaowei Zhuang" <zhua...@ccf.org> Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, March 16, 2016 11:16:48 PM Subject: Re: [Freesurfer] Hippocampal subfield segmentation with T1 Hi Xiaowei you can try mri_robust_register --cost nmi or --cost mi, then give the resulting transform to mri_convert -at transform.lta -rl T2.mgz The "-rl T2.mgz" tells mri_convert to "reslice like" the T2, so they will have the same geometry. You can also try mri_coreg if you like instead of mri_robust_register if it doesn't work well cheers Bruce On Wed, 16 Mar 2016, Zhuang, Xiaowei wrote: > > Dear Freesurfer expert, > > > > I am using Freesurfer V6.0 beta version to run the hippocampal subfield > segmentation with 2 inputs, a standard T1 and a high resolution T2. > > > > Below are the details about the 2 images. > > > > T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8) > > T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5). > > > > The instruction says in order to use both of them for hippocampal > segmentation, T2 should be in the same orientation as T1. Therefore, the two > images cannot be used directly. > > > > Is it possible for me to do some reorient preprocess on the T2 image and > then run through the segmentation? > > > > Or is it possible to coregister the T1 into T2 space, making them both high > resolution and run through the segmentation? Will this affect the Freesurfer > pipeline and the final subfields output? > > > > Any suggestion will help. > > > > Sincerely thanks, > > Xiaowei. > > > > > > > > Cleveland Clinic logo > > > > Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain > Health > > Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV > 89106 | (702) 685-6051 > > > > > > === > > Please consider the environment before printing this e-mail > > Cleveland Clinic is ranked as one of the top hospitals in America by > U.S.News & World Report (2015). Visit us online at > http://www.clevelandclinic.org for a complete listing of our services, staff > and locations. Confidentiality Note: This message is intended for use only > by the individual or entity to which it is addressed and may contain > information that is privileged, confidential, and exempt from disclosure > under applicable law. If the reader of this message is not the intended > recipient or the employee or agent responsible for delivering the message to > the intended recipient, you are hereby notified that any dissemination, > distribution or copying of this communication is strictly prohibited. If you > have received this communication in error, please contact the sender > immediately and destroy the material in its entirety, whether electronic or > hard copy. Thank you. > > ___ Freesurfer mailing list Freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampal subfield segmentation with T1
Dear Freesurfer expert, I am using Freesurfer V6.0 beta version to run the hippocampal subfield segmentation with 2 inputs, a standard T1 and a high resolution T2. Below are the details about the 2 images. T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8) T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5). The instruction says in order to use both of them for hippocampal segmentation, T2 should be in the same orientation as T1. Therefore, the two images cannot be used directly. Is it possible for me to do some reorient preprocess on the T2 image and then run through the segmentation? Or is it possible to coregister the T1 into T2 space, making them both high resolution and run through the segmentation? Will this affect the Freesurfer pipeline and the final subfields output? Any suggestion will help. Sincerely thanks, Xiaowei. [Cleveland Clinic logo] Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain Health Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV 89106 | (702) 685-6051 === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Hippocampal subfield segmentation with T1
Hi Xiaowei you can try mri_robust_register --cost nmi or --cost mi, then give the resulting transform to mri_convert -at transform.lta -rl T2.mgz The "-rl T2.mgz" tells mri_convert to "reslice like" the T2, so they will have the same geometry. You can also try mri_coreg if you like instead of mri_robust_register if it doesn't work well cheers Bruce On Wed, 16 Mar 2016, Zhuang, Xiaowei wrote: Dear Freesurfer expert, I am using Freesurfer V6.0 beta version to run the hippocampal subfield segmentation with 2 inputs, a standard T1 and a high resolution T2. Below are the details about the 2 images. T1: resolution: 0.8*0.8*0.8 mm, orientation: Sagittal(S>T4.1>C-0.8) T2: resolution: 0.4*0.4*1.5 mm, orientation: oblique coronal(C>T-14.5>S1.5). The instruction says in order to use both of them for hippocampal segmentation, T2 should be in the same orientation as T1. Therefore, the two images cannot be used directly. Is it possible for me to do some reorient preprocess on the T2 image and then run through the segmentation? Or is it possible to coregister the T1 into T2 space, making them both high resolution and run through the segmentation? Will this affect the Freesurfer pipeline and the final subfields output? Any suggestion will help. Sincerely thanks, Xiaowei. Cleveland Clinic logo Xiaowei Zhuang | Research Engineer | Lou Ruvo Center for Brain Health Cleveland Clinic | 888 W Bonneville Ave. | Las Vegas, NV 89106 | (702) 685-6051 === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@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.
