You are trying to combine data from two very different protocols. This is not advisable. I would exclude those 5 subjects.
From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Rizvi, Batool" <br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, March 29, 2017 at 10:43 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions So sorry - one last question. Would it be also ok if the value of the bval numbers are also different? One set of subjects/bvals have 15 numbers with the value of 800, while the 5 of them have the 48 numbers with value of 1000. Is this an issue as well? Thanks Dr. Yendiki, for all the help! Batool ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>] Sent: Wednesday, March 29, 2017 9:12 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions You should use the same 16 gradient directions as the ones that your 16-direction scans have. You have to look at the gradient tables from subjects with each type of scan. Once you have identified which volumes in the 49-volume series were acquired with those 16 directions, you can use something like: mri_convert --i input_dwis --f 0 5 17 --o output_dwis where you'd replace my "0 5 17" with your list of the (0-based) numbers of the volumes that you want to extract (16 numbers in your case). ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Rizvi, Batool [br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>] Sent: Wednesday, March 29, 2017 9:01 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions Thank you. That makes sense, and in that case we'll only use 16 directions for all subjects, including in those 5. Just wondering if you had any pointers on which software could be used to extract the 16 directions from the 49, or if it's ususally done by code in matlab? Also, in terms of choosing the 16 directions to pull out from these 5 files, would you use the first 16 directions in the file, or the most evenly distributed 16 directions? Thanks again! Batool ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Yendiki, Anastasia [ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>] Sent: Wednesday, March 29, 2017 8:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA - subjects with different number of directions Hi Batool - Yes, it would be a problem. It'd be similar to having some scans with one spatial resolution and some with another, or administering one questionnaire to some of your subjects and a different one to the others and then trying to compare the answers. If the 16 directions are a subset of the 49 directions, then you can discard the remaining 33 directions from the subjects that have 49. Best, a.y ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Rizvi, Batool [br2...@cumc.columbia.edu<mailto:br2...@cumc.columbia.edu>] Sent: Wednesday, March 29, 2017 8:37 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] TRACULA - subjects with different number of directions Hi, We were wondering if it would be an issue if we used a dataset in which we included 5 subjects that have a different number of directions (49 directions) than the rest of the subjects with a standard number (16 directions). Even if the preprocessing steps work, will it be an issue comparing the subjects statistically? If so, how can we treat the 5 subjects differently, but still include them in our study? Thank you! Batool
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