Re: [Freesurfer] Intensity information of Hippocampal Subfields
I processed the T1-weighted data without T2. Therefore, we do not have T2.norm.mgz in the mri folder of each subject. Only for the HP-subfields segmentation, we added additional high-resolution T2-weighted data to increase the accuracy of HP-subfields segmentation. Thanks! Alireza > On Feb 27, 2017, at 12:53 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > > There is usually a T2.norm.mgz file in the mri folder. If that is there, > then you should use that rather than the raw data that is not bias field > corrected > > >> On 02/27/2017 12:30 PM, ali reza mohammadi nejad wrote: >> Thank you so much Dr. Doug! I just have one more question: >> >> Now I want to compute the same information for our second modality (i.e., >> mean and std intensity of different HP_subfields for our additional scan, >> e,g., T2 or FLAIR). >> My question is that how could I use .FSspace.mgz (in mri folder) >> and T1_to_.v10.Ita (in transform folder) files in mri_segstats >> command? >> >> Thank you in advance for any help. >> Best regards, >> Alireza >> >> >>> On Feb 24, 2017, at 10:51 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> wrote: >>> >>> The basic command is >>> >>> mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz >>> >>> where seg is the hippo sub field seg and input is the input where you >>> want to get the intensities from (probably norm.mgz). Note that you need >>> to use the hipp sub field output that is 1mm (not the high res one) >>> >>> >>>> On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote: >>>> Dear FreeSurfer Experts, >>>> I want to compute some intensity information (e.g., mean and std) of each >>>> Hippocampal subfields (similar to aseg.stats file). >>>> I think one option could be mri_segstats command, but I am not sure. >>>> If it works, what are the inputs of this command? >>>> >>>> Thank you in advance for any help. >>>> Alireza >>>> >>>> >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> ___ >>> 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 >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Intensity information of Hippocampal Subfields
Thank you so much Dr. Doug! I just have one more question: Now I want to compute the same information for our second modality (i.e., mean and std intensity of different HP_subfields for our additional scan, e,g., T2 or FLAIR). My question is that how could I use .FSspace.mgz (in mri folder) and T1_to_.v10.Ita (in transform folder) files in mri_segstats command? Thank you in advance for any help. Best regards, Alireza > On Feb 24, 2017, at 10:51 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > > The basic command is > > mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz > > where seg is the hippo sub field seg and input is the input where you > want to get the intensities from (probably norm.mgz). Note that you need > to use the hipp sub field output that is 1mm (not the high res one) > > >> On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote: >> Dear FreeSurfer Experts, >> I want to compute some intensity information (e.g., mean and std) of each >> Hippocampal subfields (similar to aseg.stats file). >> I think one option could be mri_segstats command, but I am not sure. >> If it works, what are the inputs of this command? >> >> Thank you in advance for any help. >> Alireza >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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
Re: [Freesurfer] Intensity information of Hippocampal Subfields
Thank you so much Dr. Doug! I just have one more question: Now I want to compute the same information for our second modality (i.e., mean and std intensity of different HP_subfields for our additional scan, e,g., T2 or FLAIR).My question is that how could I use .FSspace.mgz (in mri folder) and T1_to_.v10.Ita (in transform folder) files in mri_segstats command? Thank you in advance for any help.Best regards,Alireza On Friday, February 24, 2017 10:51 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: The basic command is mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz where seg is the hippo sub field seg and input is the input where you want to get the intensities from (probably norm.mgz). Note that you need to use the hipp sub field output that is 1mm (not the high res one) On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote: > Dear FreeSurfer Experts, > I want to compute some intensity information (e.g., mean and std) of each > Hippocampal subfields (similar to aseg.stats file). > I think one option could be mri_segstats command, but I am not sure. > If it works, what are the inputs of this command? > > Thank you in advance for any help. > Alireza > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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] Intensity information of Hippocampal Subfields
Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command? Thank you in advance for any help. Alireza ___ 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] [Repost] question about mris_anatomical_stat
Dear Freesurfer experts Based on the FS wiki, I calculated the cortical thickness difference between the LH and RH of a subject in subject's native surface.Now, I want to use FS commands to extract the information such as "?h.aparc.stats" for this difference map (LH - RH).Now this difference map is saved in a .mgh file.I think, I can use "mris_anatomical_stats" command for this propose.But, based on the help of this command, I did not find any .mgh file as an input.Therefore, would you please help me to create such stats file?Thank you very much for your help Best regards,Alireza ___ 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] question about mris_anatomical_stats
Dear Freesurfer experts Based on the FS wiki, I calculated the cortical thickness difference between the LH and RH of a subject in subject's native surface.Now, I want to use FS commands to extract the information such as "?h.aparc.stats" for this difference map (LH - RH).Now this difference map is saved in a .mgh file.I think, I can use "mris_anatomical_stats" command for this propose.But, based on the help of this command, I did not find any .mgh file as an input.Therefore, would you please help me to create such stats file?Thank you very much for your help Best regards,Alireza ___ 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] mapping a surface from fsaverage_sym to the subject's native surface
Dear Freesurfer experts, > > Based on the FS wiki, I calculated the cortical thickness difference between > the lh and rh of a subject. > Now, I want to use the “mris_apply_reg” command to map the “left-right > difference” from fsaverage_sym back to the subject's native surface. > Unfortunately, I did not find the appropriate options of this command to do > this work. > Thanks for any help. > > Best regards, > Ali-Reza > > Ali-Reza Mohammadi-Nejad > Pre-doctoral research fellow > Radiology and Neurology Research > Henry Ford Health System > Detroit, MI 48202, USA ___ 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] mapping a surface from fsaverage_sym to the subject's native surface
Dear Freesurfer experts, Based on the FS wiki, I calculated the cortical thickness difference between the lh and rh of a subject.Now, I want to use the “mris_apply_reg” command to map the “left-right difference” from fsaverage_sym back to the subject's native surface.Unfortunately, I did not find the appropriate options of this command to do this work.Thanks for any help. Best regards,Ali-Reza Ali-Reza Mohammadi-Nejad Pre-doctoral research fellow Radiology and Neurology Research Henry Ford Health System Detroit, MI 48202, USA___ 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] mapping a surface from fsaverage_sym to the subject's native surface
Dear Freesurfer experts, Based on the FS wiki, I calculated the cortical thickness difference between the lh and rh of a subject. Now, I want to use the “mris_apply_reg” command to map the “left-right difference” from fsaverage_sym back to the subject's native surface. Unfortunately, I did not find the appropriate options of this command to do this. Thanks for any help. Best regards,Ali-Reza Ali-Reza Mohammadi-Nejad Pre-doctoralresearch fellow Radiology and NeurologyResearch HenryFord Health System Detroit,MI 48202, USA ___ 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] Brain extraction problem
Hi and Thank you for your response. I have 85 subjects (AD and HC) and the initial workflow of my work is: 1. Brain extraction and intensity normalization of each subject (-autorecon1) 2. Register each brain to MNI152 3. Make a global mask using all of the subjects 4. Do other parts of my algorithm. Therefore as you can see, when a lot of voxels of a subject in its brainmask.mgz is zero (we have a lot of hole), it affects the global mask of the group. Could you please help me to solve this problem. Best regards, Ali-Reza On Saturday, January 3, 2015 7:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ali-Reza I'm not sure I understand the problem. In the images you sent it looks to me like all the zero voxels are not part of brain tissue, but are rather either ventricular or sulcal csf cheers Bruce On Fri, 2 Jan 2015, Ali-Reza Mohammadi-Nejad wrote: Hi FreeSurfer experts, I am using the recon-all command to extract the brain section of each subjects. I am using the watershed option to increase the accuracy of brain extraction and I change this parameter from 1 to 50 and select the best value using visual check of the results using the following script: * recon-all -s 001 -autorecon1 * recon-all -skullstrip -wsthresh 02 -clean-bm -no-wsgcaatlas -subjid 001 For the most of my subjects, the output is very good but for 6 subjects, at the upper side of the brain, the results are bad. In the attached file, you can find the output of one of these results. As you can see, when I overlay the brainmask.mgz on the orig.mgz volume, some voxels within the brain are exactly zero on the brainmask.mgz. Would you please let me to know that how can I solve this problem? Thank you very much in advance for the help! Best, Ali-Reza ___ 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 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] Out of memory error on mri_cvs_register
Hi I am trying to do an mri_cvs_register for two subjects analyzed with FS-5.1.0 on a 64-bit CentOS linux vmware on a 64 bit windows 7 with 16GB memory. I am running a signle mri_cvs_register and after certain time the process terminates with out of memory error. I have done this work a lot of times with different preprocessed subjects. Could you please let me to know that, How can I solve this problem? Best regards, Mohammadi-Nejad ___ 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.
