I agree with Tim that parcellation is a better approach. We recommend using the HCP’s multi-modal parcellation, but you could make an evenly tessellated one too. I believe FreeSurfer has a tool for this.
Peace, Matt. From: 罗 <[email protected]<mailto:[email protected]>> Date: Monday, March 13, 2017 at 10:23 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: hcp-users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] about the PostFreeSurferPipeline Thanks for your reply It's just the HCP fMRI data, what you afford in cifti format is 96854×1200 dimension, which means too many for me, and what I want is about 600～1000×1200 demension. Best wishes! Yours ------------------ Original ------------------ From: Glasser, Matthew <[email protected]<mailto:[email protected]>> Date: 周二,3月 14,2017 11:05 上午 To: 罗 <[email protected]<mailto:[email protected]>>, NEUROSCIENCE tim <[email protected]<mailto:[email protected]>> Cc: hcp-users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] about the PostFreeSurferPipeline What is the resolution of the original volume data? Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of 罗 <[email protected]<mailto:[email protected]>> Date: Monday, March 13, 2017 at 9:54 PM To: Timothy Coalson <[email protected]<mailto:[email protected]>> Cc: hcp-users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] about the PostFreeSurferPipeline Thanks very much for your reply and suggestion! I'm doing some testing based on surface fMRI, yes, it's my intention to reduce the data dimension as much as I can in a reasonable range, taking your suggestion into account fsaverage4 is acceptable, and I will be very appreciated if I can be afforded the cifti template based on fsaverage4, what's more, if I can be told the method of making cifti templates based on FreeSurfer surface vertices and under cortical voxels it would be grateful. Parcellation, as you said, can have meaningful boundaries that separate functional areas, but what I need is a general template in which blurring is fully acceptable, while different subjects can obviously have different parcellation results and it takes time to generate a general template from these result. Best whishes and looking for your reply and suggestion! Yours ------------------ Original ------------------ From: Timothy Coalson <[email protected]<mailto:[email protected]>> Date: 周二,3月 14,2017 8:52 上午 To: 罗 <[email protected]<mailto:[email protected]>> Cc: hcp-users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] about the PostFreeSurferPipeline fsaverage3 is less than 1k vertices, and is such a low sampling on the surface that it is closer to the realm of parcellation. If you resample anatomical surfaces to something that low, some smaller folds may vanish entirely because they are skipped over by such a coarse mesh. I have attached a capture of fsaverage7 and fsaverage4 midthickness surfaces, to give you an idea - fsaverage3 would look much worse, as each triangle would be 4x bigger in area (I haven't tried to generate any). If your intention is to reduce the dimensionality of data in order to do something like graph theoretic analysis, then parcellation is probably a better option, as it can have meaningful boundaries that separate functional areas, while downsampling simply blurs things together with no respect to what signals can be shown to be of different function. Tim On Sun, Mar 12, 2017 at 11:10 PM, 罗 <[email protected]<mailto:[email protected]>> wrote: Thanks for you reply. As far as I know, the 32k vertices template is based on the fsaverage in FreeSurfer which also contains fsaverage3, fsaverage4, fsaverage5 and fsaverage6, what should I do if I want to make a template based on fsaverage3? Thanks Yours 发自我的iPhone ------------------ Original ------------------ From: Glasser, Matthew <[email protected]<mailto:[email protected]>> Date: 周一,3月 13,2017 11:13 上午 To: 罗 <[email protected]<mailto:[email protected]>>, hcp-users <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] about the PostFreeSurferPipeline That is really low. What spacing do you think would be reasonable on the cortical surface? 32k is 2mm on average. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of 罗 <[email protected]<mailto:[email protected]>> Date: Sunday, March 12, 2017 at 10:09 PM To: hcp-users <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] about the PostFreeSurferPipeline Dear professors: I'm studying the HCP Pipeline right now, and I have a question about the PostFreeSurferPipeline, in the input variables of PostFreeSurferPipeline.sh, you have set HighResMesh＝“164”, LowResMeshs＝“32”, and you noted that the lowresmeshs was usually 32k vertices, if multiple delimit with @, must already exist in templates dir, but I only find 164 and 32 in the templates dir. This is the question, if I want to set the lowresmeshs lower than 32k, for example, 1k, what should I do? And what corrdinate greyordinate should I make? Thanks very much! Yours 发自我的iPhone _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users Spam detection software, running on the system "mailman02.nrg.mir", has identified this incoming email as possible spam. The original message has been attached to this so you can view it (if it isn't spam) or label similar future email. If you have any questions, see @@CONTACT_ADDRESS@@ for details. Content preview: Thanks for you reply. As far as I know, the 32k vertices template is based on the fsaverage in FreeSurfer which also contains fsaverage3, fsaverage4, fsaverage5 and fsaverage6, what should I do if I want to make a template based on fsaverage3? 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As far as I know, the 32k vertices template is based on the fsaverage in FreeSurfer which also contains fsaverage3, fsaverage4, fsaverage5 and fsaverage6, what should I do if I want to make a template based on fsaverage3? Thanks Yours [...] Content analysis details: (8.5 points, 5.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 2.8 FROM_STARTS_WITH_NUMS From: starts with many numbers 3.2 CHARSET_FARAWAY_HEADER A foreign language charset used in headers 0.0 HTML_MESSAGE BODY: HTML included in message 2.5 MIME_CHARSET_FARAWAY MIME character set indicates foreign language _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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