Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca
Hi Bruce, I'll have a look at mri_ca_train. Thanks again! Cheers, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl [fis...@nmr.mgh.harvard.edu] Verzonden: donderdag 25 februari 2016 20:58 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca Hi Jelmer no, that won't work as the gca contains more information than that. YOu will need to use mri_ca_train to create a new gca, which should be relatively straightforward cheers Bruce On Thu, 25 Feb 2016, Kok, JG (neuro) wrote: > Hi Bruce, > > Thanks for your quick reply. I do not have manually split asegs, I wish to > create them all automatically. I'm hoping it is possible to read > RB_all_2008-03-26.gca (preferably in MATLAB, using fread), and adjust all > putamen values posterior from the coronal plane through the anterior > commissure from (FreeSurferColorLUT)values 12 and 51 to for example values > 10012 and 10051 (and subsequently save the new file with fwrite). Do you > think this is possible? > > Cheers, > > Jelmer > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Verzonden: donderdag 25 februari 2016 20:32 > Aan: Freesurfer support list > Onderwerp: Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca > > Hi Jelmer > > if you have manually split asegs you can use them as input to mri_ca_train > to create a new gca that has the separated putamen. You'll need to add a > couple of entries to FreeSurferColorLUT.txt to specify how to display and > name the new entries as well > > cheers > Bruce > > On Thu, 25 Feb 2016, Kok, JG (neuro) wrote: > >> Hi, >> >> I wish to split the putamen in an anterior part and a posterior part in >60 >> subjects which have been analyzed by the recon-all stream (FS version >> 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the >> coronal plane through the anterior commissure) and apply this "new" atlas to >> all subjects, one of the advantages being the bias that would be introduced >> by splitting the putamena manually in all subjects would be avoided. After >> some time trying to make this happen, I now think this could be achieved by >> adjusting RB_all_2008-03-26.gca and applying something like >> >> "mri_ca_label -align subject_norm.mgz subject_talairach.m3z >> RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz". >> >> The problem is that till now I wasn't able to figure out how to correctly >> read the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB >> function load_gca.m, but that seems to only work up to version 4 of the .gca >> file format (as GCA_VERSION is set to 4 in the function), and >> RB_all_2008-03-26.gca seems to be version 5. Also, when trying to read the >> file anyway in MATLAB using the code written for version 4 and below (by >> setting GCA_VERSION to 5.0), the code fails (the first gibbs_nlabels is >> already way too large, although I suspect the error occurs earlier). >> >> My questions: >> 1. Do you think I am following the right track to achieve a sensible >> splitting of the putamena this way? Or should I try something else? >> 2. Is there a newer load_gca.m file around which is able to read a version 5 >> .gca file? Or could you point me to the difference in the design of the >> version 5 .gca file compared to that of the version 4 file so that I can >> rewrite load_gca.m? >> >> Cheers, >> >> Jelmer >> >> >> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de >> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken >> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of >> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een >> incomplete aankomst of vertraging van dit verzonden bericht. >> >> The contents of this message are confidential and only intended for the eyes >> of the addressee(s). Others than the addressee(s) are not allowed to use >> this message, to make it public or to distribute or multiply this message in >> any way. The UMCG cannot be held responsible for incomplete reception or >> delay of this transferred message. >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > htt
Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca
Hi Bruce, Thanks for your quick reply. I do not have manually split asegs, I wish to create them all automatically. I'm hoping it is possible to read RB_all_2008-03-26.gca (preferably in MATLAB, using fread), and adjust all putamen values posterior from the coronal plane through the anterior commissure from (FreeSurferColorLUT)values 12 and 51 to for example values 10012 and 10051 (and subsequently save the new file with fwrite). Do you think this is possible? Cheers, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl [fis...@nmr.mgh.harvard.edu] Verzonden: donderdag 25 februari 2016 20:32 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca Hi Jelmer if you have manually split asegs you can use them as input to mri_ca_train to create a new gca that has the separated putamen. You'll need to add a couple of entries to FreeSurferColorLUT.txt to specify how to display and name the new entries as well cheers Bruce On Thu, 25 Feb 2016, Kok, JG (neuro) wrote: > Hi, > > I wish to split the putamen in an anterior part and a posterior part in >60 > subjects which have been analyzed by the recon-all stream (FS version > 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the > coronal plane through the anterior commissure) and apply this "new" atlas to > all subjects, one of the advantages being the bias that would be introduced > by splitting the putamena manually in all subjects would be avoided. After > some time trying to make this happen, I now think this could be achieved by > adjusting RB_all_2008-03-26.gca and applying something like > > "mri_ca_label -align subject_norm.mgz subject_talairach.m3z > RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz". > > The problem is that till now I wasn't able to figure out how to correctly > read the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB > function load_gca.m, but that seems to only work up to version 4 of the .gca > file format (as GCA_VERSION is set to 4 in the function), and > RB_all_2008-03-26.gca seems to be version 5. Also, when trying to read the > file anyway in MATLAB using the code written for version 4 and below (by > setting GCA_VERSION to 5.0), the code fails (the first gibbs_nlabels is > already way too large, although I suspect the error occurs earlier). > > My questions: > 1. Do you think I am following the right track to achieve a sensible > splitting of the putamena this way? Or should I try something else? > 2. Is there a newer load_gca.m file around which is able to read a version 5 > .gca file? Or could you point me to the difference in the design of the > version 5 .gca file compared to that of the version 4 file so that I can > rewrite load_gca.m? > > Cheers, > > Jelmer > > > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de > geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken > van dit bericht, het niet openbaar maken of op enige wijze verspreiden of > vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een > incomplete aankomst of vertraging van dit verzonden bericht. > > The contents of this message are confidential and only intended for the eyes > of the addressee(s). Others than the addressee(s) are not allowed to use > this message, to make it public or to distribute or multiply this message in > any way. The UMCG cannot be held responsible for incomplete reception or > delay of this transferred message. > ___ 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. De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to
Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points
Hi Ed, I'm not sure if this'll help you, but I read your question right after I posted mine, and thought to let you know the solution I used in cases where I had to add control points: " Or Make Life Easier recon-all -make all -s subjid " is copied from one of the Freesurfer Powerpoint slides. It worked great for me, and I suspect it will also work in your case. As far as I understand, using this command Freesurfer will look for the first function in the pipeline where some of the input has been modified, and performs all recon-all steps from there. Cheers, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Gronenschild Ed (NP) [ed.gronensch...@maastrichtuniversity.nl] Verzonden: donderdag 25 februari 2016 19:19 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: [Freesurfer] How to invoke skullstrip adjustments and wm control points Hi, I have made some manual skullstrip adjustments and added a number of control points in the white matter. How should I proceed with recon-all to incorporate both adjustments? Cheers, Ed ___ 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. De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Minor adjustment to RB_all_2008-03-26.gca
Hi, I wish to split the putamen in an anterior part and a posterior part in >60 subjects which have been analyzed by the recon-all stream (FS version 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the coronal plane through the anterior commissure) and apply this "new" atlas to all subjects, one of the advantages being the bias that would be introduced by splitting the putamena manually in all subjects would be avoided. After some time trying to make this happen, I now think this could be achieved by adjusting RB_all_2008-03-26.gca and applying something like "mri_ca_label -align subject_norm.mgz subject_talairach.m3z RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz". The problem is that till now I wasn't able to figure out how to correctly read the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB function load_gca.m, but that seems to only work up to version 4 of the .gca file format (as GCA_VERSION is set to 4 in the function), and RB_all_2008-03-26.gca seems to be version 5. Also, when trying to read the file anyway in MATLAB using the code written for version 4 and below (by setting GCA_VERSION to 5.0), the code fails (the first gibbs_nlabels is already way too large, although I suspect the error occurs earlier). My questions: 1. Do you think I am following the right track to achieve a sensible splitting of the putamena this way? Or should I try something else? 2. Is there a newer load_gca.m file around which is able to read a version 5 .gca file? Or could you point me to the difference in the design of the version 5 .gca file compared to that of the version 4 file so that I can rewrite load_gca.m? Cheers, Jelmer De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ___ 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] PVC correction - estimation release version 6
Dear Freesurfer experts, I would be very interested in using the PVC correction software for PET images, that will be available within Freesurfer version 6. Would you be able to estimate a date for the release of the stable release of version 6 (I realize this may be difficult)? Depending on your estimation I may wait for this release, or keep using 5.3.0 for segmentation of the T1 image (and try to find PVC correction somewhere else). Best, Jelmer De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ___ 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] quality T1 for new study
Hi Bruce, Many thanks for your reply. I did run it through recon-all and it seems to give nice results. Still, as I am just a beginner using Freesurfer, I would greatly appreciate it when you would have a look at the output which can be downloaded from 'http://gate.nmr.mgh.harvard.edu/filedrop2/?p=69915f8pefn'. Cheers, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl [fis...@nmr.mgh.harvard.edu] Verzonden: vrijdag 18 april 2014 15:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 for new study Hi Jelmer the scan looks quite nice to me. Have you run it through recon-all? That is the best way to get an idea of how well it will work. cheers Bruce On Fri, 18 Apr 2014, Kok, JG (neuro) wrote: > Dear Freesurfer experts, > > I uploaded a .nii.gz file (which can be downloaded from > 'http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7pbsgklemux'). I hope you > would be willing to comment on the quality of this scan for use with > Freesurfer (you can find some parameters below; the scan > was acquired on a 3T Philips scanner). Running it through recon-all seems to > give nice results, but then again, I am in a phase > of running pilots before the start of a new study, and I do not have much > experience with Freesurfer results yet. > > coil: 32 channel > Sequence: T1w_TFE_3D > TFE factor: 256 > Acquisition time: 10:14 > FoV FH256xAP256xRL160 mm > 160 sagittal slices > fold-over direction AP > fat shift direction F > scan mode 3D > > acquisition matrix 256 x 256 > acquisition voxel size 1.00/1.00/1.00 > reconstructed voxel size 1.00/1.00/1.00 > TR shortest (=7.6ms) > TE shortest (=3.5ms) > RF: flip angle 8 degrees > Acceleration: no SENSE > inversion-prepared, inversion delay time: shortest > > Cheers, > > Jelmer Kok > > > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de > geadresseerde(n). Anderen dan de geadresseerde(n) mogen > geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze > verspreiden of vermenigvuldigen. Het UMCG kan niet > aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van > dit verzonden bericht. > > The contents of this message are confidential and only intended for the eyes > of the addressee(s). Others than the addressee(s) > are not allowed to use this message, to make it public or to distribute or > multiply this message in any way. The UMCG cannot be > held responsible for incomplete reception or delay of this transferred > message. > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ___ 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] quality T1 for new study
Dear Freesurfer experts, I uploaded a .nii.gz file (which can be downloaded from 'http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7pbsgklemux'). I hope you would be willing to comment on the quality of this scan for use with Freesurfer (you can find some parameters below; the scan was acquired on a 3T Philips scanner). Running it through recon-all seems to give nice results, but then again, I am in a phase of running pilots before the start of a new study, and I do not have much experience with Freesurfer results yet. coil: 32 channel Sequence: T1w_TFE_3D TFE factor: 256 Acquisition time: 10:14 FoV FH256xAP256xRL160 mm 160 sagittal slices fold-over direction AP fat shift direction F scan mode 3D acquisition matrix 256 x 256 acquisition voxel size 1.00/1.00/1.00 reconstructed voxel size 1.00/1.00/1.00 TR shortest (=7.6ms) TE shortest (=3.5ms) RF: flip angle 8 degrees Acceleration: no SENSE inversion-prepared, inversion delay time: shortest Cheers, Jelmer Kok De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ___ 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] quality T1 scans for new study
Great, thanks again! Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl [fis...@nmr.mgh.harvard.edu] Verzonden: woensdag 2 april 2014 18:22 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study sure, that would be fine. Upload teh whole dataset and we will take a look Bruce On Wed, 2 Apr 2014, Kok, JG (neuro) wrote: > Hi Bruce, > > Thank you very much for your time. I was just talking to our physicist on > this subject, and he said, as you judge the quality of a sequence by its > parameters, it may make more sense to run a scan using the parameters as > proposed by Freesurfer for Philips (as in the body of the email yesterday) > than to ask you to comment on our parameters. > > As I agree that may be more sensible, we will try that first. Thank you very > much for your considerations (so far)! > > Cheers, > > Jelmer > > > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Verzonden: woensdag 2 april 2014 14:30 > Aan: Freesurfer support list > CC: Andre van der Kouwe > Onderwerp: Re: [Freesurfer] quality T1 scans for new study > > Hi Jelmer > > I took a quick look, but it is a lot easier for us if you extract the > relevant parameters, as we are not that familiar with Philips in general. > Is this inversion-prepared? I didn't see a TI. Generally > inversion-preparation improves T1 CNR/unit-time. Also, your wrap direction > looks like it is A/P.You might try making it L/R instead which is a shorter > dimension. What coil are you using? Are you using sense? > > cheers > Bruce > > > On Wed, 2 Apr 2014, Kok, JG (neuro) wrote: > >> Dear Bruce, Andre, someone else, >> >> I think I caused some misunderstanding yesterday for which I am sorry. Now I >> do not know on what parameters Andre commented. So to hopefully make things >> clear I am once more attaching the parameter file which was used to create a >> T1 image (see attached screenshots) that may be of good quality. I hope you >> are willing to have a look and see if these parameters would result in good >> quaity T1 images. >> >> Thanks, >> >> Jelmer >> >> >> >> Van: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) >> [j.g.ko...@umcg.nl] >> Verzonden: dinsdag 1 april 2014 18:17 >> Aan: Freesurfer support list >> Onderwerp: Re: [Freesurfer] quality T1 scans for new study >> >> Hi Andre, >> >> I hope you looked at the attached "scan1_parameter_file.txt" when you >> mentioned that you think it seemed to be a reasonable protocol: the >> parameters in the body of the email Bruce is referring to were the suggested >> parameters in >> "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf";, >> not the ones I am using/planning to adjust. >> >> Thanks, >> >> Jelmer >> >> >> >> Van: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Verzonden: dinsdag 1 april 2014 18:10 >> Aan: Freesurfer support list >> CC: Andre van der Kouwe >> Onderwerp: Re: [Freesurfer] quality T1 scans for new study >> >> no, I just looked at the ones in the body of your email >> On Tue, 1 Apr 2014, >> Kok, JG (neuro) wrote: >> >>> Dear Bruce and Andre, >>> >>> PS I am sorry, but may I assume you have only looked at the parameters in >>> "scan1_parameter_file.txt" and not in >>> "scan2_parameter_file.txt"? That would be fine, but I would just like to >>> check we are talking about the same scan parameters >>> that seem to be fine... >>> >>> Thanks, >>> >>> Jelmer >>> >>> >>> Van: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) >>> [j.g.ko...@umcg.nl] >>> Verzonden: dinsdag 1 april 2014 16:45 >>> Aan: Freesurfer support list >>> Onderwerp: Re: [Freesurfer] quality T1 scans for new study >>> >>> Hi Bruce and Andre, >>>
Re: [Freesurfer] quality T1 scans for new study
Hi Bruce, Thank you very much for your time. I was just talking to our physicist on this subject, and he said, as you judge the quality of a sequence by its parameters, it may make more sense to run a scan using the parameters as proposed by Freesurfer for Philips (as in the body of the email yesterday) than to ask you to comment on our parameters. As I agree that may be more sensible, we will try that first. Thank you very much for your considerations (so far)! Cheers, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl [fis...@nmr.mgh.harvard.edu] Verzonden: woensdag 2 april 2014 14:30 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study Hi Jelmer I took a quick look, but it is a lot easier for us if you extract the relevant parameters, as we are not that familiar with Philips in general. Is this inversion-prepared? I didn't see a TI. Generally inversion-preparation improves T1 CNR/unit-time. Also, your wrap direction looks like it is A/P.You might try making it L/R instead which is a shorter dimension. What coil are you using? Are you using sense? cheers Bruce On Wed, 2 Apr 2014, Kok, JG (neuro) wrote: > Dear Bruce, Andre, someone else, > > I think I caused some misunderstanding yesterday for which I am sorry. Now I > do not know on what parameters Andre commented. So to hopefully make things > clear I am once more attaching the parameter file which was used to create a > T1 image (see attached screenshots) that may be of good quality. I hope you > are willing to have a look and see if these parameters would result in good > quaity T1 images. > > Thanks, > > Jelmer > > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) > [j.g.ko...@umcg.nl] > Verzonden: dinsdag 1 april 2014 18:17 > Aan: Freesurfer support list > Onderwerp: Re: [Freesurfer] quality T1 scans for new study > > Hi Andre, > > I hope you looked at the attached "scan1_parameter_file.txt" when you > mentioned that you think it seemed to be a reasonable protocol: the > parameters in the body of the email Bruce is referring to were the suggested > parameters in > "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf";, > not the ones I am using/planning to adjust. > > Thanks, > > Jelmer > > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Verzonden: dinsdag 1 april 2014 18:10 > Aan: Freesurfer support list > CC: Andre van der Kouwe > Onderwerp: Re: [Freesurfer] quality T1 scans for new study > > no, I just looked at the ones in the body of your email > On Tue, 1 Apr 2014, > Kok, JG (neuro) wrote: > >> Dear Bruce and Andre, >> >> PS I am sorry, but may I assume you have only looked at the parameters in >> "scan1_parameter_file.txt" and not in >> "scan2_parameter_file.txt"? That would be fine, but I would just like to >> check we are talking about the same scan parameters >> that seem to be fine... >> >> Thanks, >> >> Jelmer >> >> >> Van: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) >> [j.g.ko...@umcg.nl] >> Verzonden: dinsdag 1 april 2014 16:45 >> Aan: Freesurfer support list >> Onderwerp: Re: [Freesurfer] quality T1 scans for new study >> >> Hi Bruce and Andre, >> >> Many thanks for your comments! >> >> Cheers, >> >> Jelmer >> >> >> Van: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Andre van der Kouwe >> [an...@nmr.mgh.harvard.edu] >> Verzonden: dinsdag 1 april 2014 15:37 >> Aan: Bruce Fischl; Freesurfer support list >> Onderwerp: Re: [Freesurfer] quality T1 scans for new study >> >> No, I think that's a reasonable protocol to use and good to use SENSE to >> speed it up. >> >> Original message >> From: Bruce Fischl >> Date:04/01/2014 2:28 PM (GMT+02:00) >> To: Freesurfer support list >> Cc: Andre van der Kouwe
Re: [Freesurfer] quality T1 scans for new study
Hi Andre, I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is referring to were the suggested parameters in "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf";, not the ones I am using/planning to adjust. Thanks, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl [fis...@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 18:10 Aan: Freesurfer support list CC: Andre van der Kouwe Onderwerp: Re: [Freesurfer] quality T1 scans for new study no, I just looked at the ones in the body of your email On Tue, 1 Apr 2014, Kok, JG (neuro) wrote: > Dear Bruce and Andre, > > PS I am sorry, but may I assume you have only looked at the parameters in > "scan1_parameter_file.txt" and not in > "scan2_parameter_file.txt"? That would be fine, but I would just like to > check we are talking about the same scan parameters > that seem to be fine... > > Thanks, > > Jelmer > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) > [j.g.ko...@umcg.nl] > Verzonden: dinsdag 1 april 2014 16:45 > Aan: Freesurfer support list > Onderwerp: Re: [Freesurfer] quality T1 scans for new study > > Hi Bruce and Andre, > > Many thanks for your comments! > > Cheers, > > Jelmer > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Andre van der Kouwe > [an...@nmr.mgh.harvard.edu] > Verzonden: dinsdag 1 april 2014 15:37 > Aan: Bruce Fischl; Freesurfer support list > Onderwerp: Re: [Freesurfer] quality T1 scans for new study > > No, I think that's a reasonable protocol to use and good to use SENSE to > speed it up. > > Original message > From: Bruce Fischl > Date:04/01/2014 2:28 PM (GMT+02:00) > To: Freesurfer support list > Cc: Andre van der Kouwe > Subject: Re: [Freesurfer] quality T1 scans for new study > > looks pretty reasonable. Andre: any comments/suggestions? > > On Tue, 1 Apr > 2014, Kok, JG (neuro) wrote: > > > Hi Bruce, > > > > Thanks for your fast reply. > > > > Hereby I attach the parameter files of both scans (although I suspect > > looking at the parameters of "scan1" may be sufficient). > Checking it with the information on Philips at > "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf": > > > > " > > Sequence: T1W_3D_TFE_SENSE > > Acquisition time: 5:13 > > Voxel size: 1.0 x 1.0 x 1.0 mm3 > > Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice > > thickness 1 mm, (3D encoding) > > Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth > > 191.5 Hz/px > > RF: flip angle 7° > > Acceleration: 2x SENSE > > " > > > > suggests that parameters in "scan1_parameter_file.txt" are already pretty > > similar to those I guess. (Is it the SENSE that is > missing in our protocol that is the most important difference?) > > > > Thanks, > > > > Jelmer > > > > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > > Verzonden: dinsdag 1 april 2014 14:09 > > Aan: Freesurfer support list > > Onderwerp: Re: [Freesurfer] quality T1 scans for new study > > > > Hi Jelmer > > > > if you give us the specific acquisition details we can help more (receive > > coil, acceleration, voxel size, sequence type, TR/TE/TI/flip > > angle/bandwidth, etc). We also have recommended morphometry sequences > > on our website. > > > > 10 min is a pretty long structural scan for a modern MRI scanner. > > > > cheers > > Bruce > > > > On Tue, 1 Apr 2014, > > Kok, JG (neuro) wrote: > > > >> Dear Freesurfer experts, > >> We are planning to start a new MRI study which will include T1 scans. As we > >> are in a testing phase now, I was wondering whether you could comment
Re: [Freesurfer] quality T1 scans for new study
Dear Bruce and Andre, PS I am sorry, but may I assume you have only looked at the parameters in "scan1_parameter_file.txt" and not in "scan2_parameter_file.txt"? That would be fine, but I would just like to check we are talking about the same scan parameters that seem to be fine... Thanks, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) [j.g.ko...@umcg.nl] Verzonden: dinsdag 1 april 2014 16:45 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study Hi Bruce and Andre, Many thanks for your comments! Cheers, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Andre van der Kouwe [an...@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study No, I think that's a reasonable protocol to use and good to use SENSE to speed it up. Original message From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study looks pretty reasonable. Andre: any comments/suggestions? On Tue, 1 Apr 2014, Kok, JG (neuro) wrote: > Hi Bruce, > > Thanks for your fast reply. > > Hereby I attach the parameter files of both scans (although I suspect looking > at the parameters of "scan1" may be sufficient). Checking it with the > information on Philips at > "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf": > > " > Sequence: T1W_3D_TFE_SENSE > Acquisition time: 5:13 > Voxel size: 1.0 x 1.0 x 1.0 mm3 > Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness > 1 mm, (3D encoding) > Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth > 191.5 Hz/px > RF: flip angle 7° > Acceleration: 2x SENSE > " > > suggests that parameters in "scan1_parameter_file.txt" are already pretty > similar to those I guess. (Is it the SENSE that is missing in our protocol > that is the most important difference?) > > Thanks, > > Jelmer > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Verzonden: dinsdag 1 april 2014 14:09 > Aan: Freesurfer support list > Onderwerp: Re: [Freesurfer] quality T1 scans for new study > > Hi Jelmer > > if you give us the specific acquisition details we can help more (receive > coil, acceleration, voxel size, sequence type, TR/TE/TI/flip > angle/bandwidth, etc....). We also have recommended morphometry sequences > on our website. > > 10 min is a pretty long structural scan for a modern MRI scanner. > > cheers > Bruce > > On Tue, 1 Apr 2014, > Kok, JG (neuro) wrote: > >> Dear Freesurfer experts, >> We are planning to start a new MRI study which will include T1 scans. As we >> are in a testing phase now, I was wondering whether you could comment on the >> attached screenshots. Clearly, "scan1" has a better white matter/grey matter >> contrast than "scan2". Do you think going for "scan1" would be the sensible >> thing to do when we later wish to use Freesurfer with these scans? Or >> perhaps is neither of the examples I attached good enough? >> >> By the way, these scans were acquired on a Philips 3T scanner, both taking >> around 10 minutes. >> >> It you need any more information, please let me know. Many thanks in advance >> for your advice. >> >> Jelmer Kok >> >> >> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de >> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken >> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of >> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een >> incomplete aankomst of vertraging van dit verzonden bericht. >> >> The contents of this message are confidential and only intended for the eyes >> of the addressee(s). Others than the addressee(s) are not allowed to use >> this message, to make it public or to distribute or multiply this message in >> any way. The UMCG cannot be held responsible for incomplete reception or >> delay of this transferred message. >> > ___ > Freesurfer mailing list > Freesurfer@nmr.m
Re: [Freesurfer] quality T1 scans for new study
Hi Bruce and Andre, Many thanks for your comments! Cheers, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Andre van der Kouwe [an...@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 15:37 Aan: Bruce Fischl; Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study No, I think that's a reasonable protocol to use and good to use SENSE to speed it up. Original message From: Bruce Fischl Date:04/01/2014 2:28 PM (GMT+02:00) To: Freesurfer support list Cc: Andre van der Kouwe Subject: Re: [Freesurfer] quality T1 scans for new study looks pretty reasonable. Andre: any comments/suggestions? On Tue, 1 Apr 2014, Kok, JG (neuro) wrote: > Hi Bruce, > > Thanks for your fast reply. > > Hereby I attach the parameter files of both scans (although I suspect looking > at the parameters of "scan1" may be sufficient). Checking it with the > information on Philips at > "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf": > > " > Sequence: T1W_3D_TFE_SENSE > Acquisition time: 5:13 > Voxel size: 1.0 x 1.0 x 1.0 mm3 > Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness > 1 mm, (3D encoding) > Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth > 191.5 Hz/px > RF: flip angle 7° > Acceleration: 2x SENSE > " > > suggests that parameters in "scan1_parameter_file.txt" are already pretty > similar to those I guess. (Is it the SENSE that is missing in our protocol > that is the most important difference?) > > Thanks, > > Jelmer > > > Van: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Verzonden: dinsdag 1 april 2014 14:09 > Aan: Freesurfer support list > Onderwerp: Re: [Freesurfer] quality T1 scans for new study > > Hi Jelmer > > if you give us the specific acquisition details we can help more (receive > coil, acceleration, voxel size, sequence type, TR/TE/TI/flip > angle/bandwidth, etc). We also have recommended morphometry sequences > on our website. > > 10 min is a pretty long structural scan for a modern MRI scanner. > > cheers > Bruce > > On Tue, 1 Apr 2014, > Kok, JG (neuro) wrote: > >> Dear Freesurfer experts, >> We are planning to start a new MRI study which will include T1 scans. As we >> are in a testing phase now, I was wondering whether you could comment on the >> attached screenshots. Clearly, "scan1" has a better white matter/grey matter >> contrast than "scan2". Do you think going for "scan1" would be the sensible >> thing to do when we later wish to use Freesurfer with these scans? Or >> perhaps is neither of the examples I attached good enough? >> >> By the way, these scans were acquired on a Philips 3T scanner, both taking >> around 10 minutes. >> >> It you need any more information, please let me know. Many thanks in advance >> for your advice. >> >> Jelmer Kok >> >> >> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de >> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken >> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of >> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een >> incomplete aankomst of vertraging van dit verzonden bericht. >> >> The contents of this message are confidential and only intended for the eyes >> of the addressee(s). Others than the addressee(s) are not allowed to use >> this message, to make it public or to distribute or multiply this message in >> any way. The UMCG cannot be held responsible for incomplete reception or >> delay of this transferred message. >> > ___ > 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. > > > De inh
Re: [Freesurfer] quality T1 scans for new study
Hi Bruce, Thanks for your fast reply. Hereby I attach the parameter files of both scans (although I suspect looking at the parameters of "scan1" may be sufficient). Checking it with the information on Philips at "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf": " Sequence: T1W_3D_TFE_SENSE Acquisition time: 5:13 Voxel size: 1.0 x 1.0 x 1.0 mm3 Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 mm, (3D encoding) Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 191.5 Hz/px RF: flip angle 7° Acceleration: 2x SENSE " suggests that parameters in "scan1_parameter_file.txt" are already pretty similar to those I guess. (Is it the SENSE that is missing in our protocol that is the most important difference?) Thanks, Jelmer Van: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl [fis...@nmr.mgh.harvard.edu] Verzonden: dinsdag 1 april 2014 14:09 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] quality T1 scans for new study Hi Jelmer if you give us the specific acquisition details we can help more (receive coil, acceleration, voxel size, sequence type, TR/TE/TI/flip angle/bandwidth, etc). We also have recommended morphometry sequences on our website. 10 min is a pretty long structural scan for a modern MRI scanner. cheers Bruce On Tue, 1 Apr 2014, Kok, JG (neuro) wrote: > Dear Freesurfer experts, > We are planning to start a new MRI study which will include T1 scans. As we > are in a testing phase now, I was wondering whether you could comment on the > attached screenshots. Clearly, "scan1" has a better white matter/grey matter > contrast than "scan2". Do you think going for "scan1" would be the sensible > thing to do when we later wish to use Freesurfer with these scans? Or > perhaps is neither of the examples I attached good enough? > > By the way, these scans were acquired on a Philips 3T scanner, both taking > around 10 minutes. > > It you need any more information, please let me know. Many thanks in advance > for your advice. > > Jelmer Kok > > > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de > geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken > van dit bericht, het niet openbaar maken of op enige wijze verspreiden of > vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een > incomplete aankomst of vertraging van dit verzonden bericht. > > The contents of this message are confidential and only intended for the eyes > of the addressee(s). Others than the addressee(s) are not allowed to use > this message, to make it public or to distribute or multiply this message in > any way. The UMCG cannot be held responsible for incomplete reception or > delay of this transferred message. > ___ 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. De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. Coil selection 1 = "SENSE-Head-32P"; element selection ="selection 1"; Coil selection 2 = "SENSE-Head-32AH"; element selection ="selection 1"; Dual coil = "yes"; Homogeneity correction ="none"; CLEAR = "yes"; body tuned ="no"; FOV RL (mm) = 256; AP (mm) = 224; FH (mm) = 160
