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Hi,
When I examined the 18 tracts of /dpath results, a few subjects were found missing one tract but differently, for example, fmajor were missing for one subject and the other one was missing lh.slfp and rh.slfp. I was thinking could it be that AP-PA was flipped. Attached screenshots of dtifit_FA.nii, aparc+seg_mask.nii, and bvec. Can you provide some information about the flip so that I can examine it for the rest of the subjects?
Best, Qi
Hi Qi - Are those two images in the same space, or in different spaces (the aparc+aseg_mask in T1 space and the FA map in diffusion space)? If the latter is true, there is no reason to expect them to have the same orientation. Checking the registration between T1 and diffusion space is a sensible thing to do, but then you should compare the FA map to the aparc+aseg files in the dlabel/diff/ directory. The latter have been mapped from T1 to diffusion space, so they should have the same orientation as the FA map.
Best, Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Qi qi.zeng@icahn.mssm.edu Sent: Tuesday, August 25, 2020 11:07 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] missing one tract but differently for a few subjects
External Email - Use Caution
Hi,
When I examined the 18 tracts of /dpath results, a few subjects were found missing one tract but differently, for example, fmajor were missing for one subject and the other one was missing lh.slfp and rh.slfp. I was thinking could it be that AP-PA was flipped. Attached screenshots of dtifit_FA.nii, aparc+seg_mask.nii, and bvec. Can you provide some information about the flip so that I can examine it for the rest of the subjects?
Best, Qi
External Email - Use Caution
Hi Anastasia,
Yes, I checked the dtifit_FA.nii and dlabel/diff/aparc_aseg_mask_brr.nii. They are in the same direction. Attached below. However, because the tracts are missing for some subjects are fmajor and slfp. One passes the frontal lobe, which is usually blurred in AP image and another is passing occipital lobe, blurred in PA image. As I used dcm2nii to convert DICOM to nii.gz in the first place, which function already combines both AP and PA. I was wondering what could cause missing tracts in subjects. Could it be something with the Orig.nii.gz in the first place or during the process? Thank you so much!
Best, Qi
On Wed, Aug 26, 2020 at 10:22 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Qi - Are those two images in the same space, or in different spaces (the aparc+aseg_mask in T1 space and the FA map in diffusion space)? If the latter is true, there is no reason to expect them to have the same orientation. Checking the registration between T1 and diffusion space is a sensible thing to do, but then you should compare the FA map to the aparc+aseg files in the dlabel/diff/ directory. The latter have been mapped from T1 to diffusion space, so they should have the same orientation as the FA map.
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < qi.zeng@icahn.mssm.edu> *Sent:* Tuesday, August 25, 2020 11:07 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] missing one tract but differently for a few subjects
External Email - Use CautionHi,
When I examined the 18 tracts of /dpath results, a few subjects were found missing one tract but differently, for example, fmajor were missing for one subject and the other one was missing lh.slfp and rh.slfp. I was thinking could it be that AP-PA was flipped. Attached screenshots of dtifit_FA.nii, aparc+seg_mask.nii, and bvec. Can you provide some information about the flip so that I can examine it for the rest of the subjects?
Best, Qi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Qi - If understand this correctly, you have diffusion images collected with 2 different phase-encode directions, AP and PA?
If so, you shouldn't simply concatenate them. As you point out, they will be distorted in different directions. When people collect images that way, it's because they plan to use topup to correct the distortions. If you want to do that, you should use the new beta version of TRACULA. See "beta version available as..." for how to download it:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Best, Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Qi qi.zeng@icahn.mssm.edu Sent: Thursday, August 27, 2020 2:21 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] missing one tract but differently for a few subjects
External Email - Use Caution
Hi Anastasia,
Yes, I checked the dtifit_FA.nii and dlabel/diff/aparc_aseg_mask_brr.nii. They are in the same direction. Attached below. However, because the tracts are missing for some subjects are fmajor and slfp. One passes the frontal lobe, which is usually blurred in AP image and another is passing occipital lobe, blurred in PA image. As I used dcm2nii to convert DICOM to nii.gz in the first place, which function already combines both AP and PA. I was wondering what could cause missing tracts in subjects. Could it be something with the Orig.nii.gz in the first place or during the process? Thank you so much!
Best, Qi
On Wed, Aug 26, 2020 at 10:22 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Qi - Are those two images in the same space, or in different spaces (the aparc+aseg_mask in T1 space and the FA map in diffusion space)? If the latter is true, there is no reason to expect them to have the same orientation. Checking the registration between T1 and diffusion space is a sensible thing to do, but then you should compare the FA map to the aparc+aseg files in the dlabel/diff/ directory. The latter have been mapped from T1 to diffusion space, so they should have the same orientation as the FA map.
Best, Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Sent: Tuesday, August 25, 2020 11:07 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] missing one tract but differently for a few subjects
External Email - Use Caution
Hi,
When I examined the 18 tracts of /dpath results, a few subjects were found missing one tract but differently, for example, fmajor were missing for one subject and the other one was missing lh.slfp and rh.slfp. I was thinking could it be that AP-PA was flipped. Attached screenshots of dtifit_FA.nii, aparc+seg_mask.nii, and bvec. Can you provide some information about the flip so that I can examine it for the rest of the subjects?
Best, Qi
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ph.D. candidate Icahn School of Medicine at Mount Sinai
freesurfer@nmr.mgh.harvard.edu
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Yendiki, Anastasia -
Zeng, Qi