Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution
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Hi,
We collected an MP-RAGE scan at .6mm isotropic resolution with the TR bumped up to TR=5. Subject motion artifacts were mitigated by using a KinetiCor motion correction system. We followed the recommendations for processing submillimeter scans described in the FreeSurfer Wiki i.e. we added the -cm flag to recon-all and included the mris_inflate -n 100 expert option. The attached PDF of the white matter surfaces shows that they appear to be underestimated. The surface estimates fall short of the actual grey/white matter boundary. Arrows point to the most affected areas and the second image is the same as the first but without the yellow white matter surface line. FTP is disabled on my government computer. Please specify the recipient email if I have to transfer the file using FileDrop. Could you suggest other options either at the time of scanning or in running recon-all that could help better segment the white matter?
Thanks,
François Lalonde, Ph.D. DNU/HGB/NIMH/NIH 10 Center Drive, Room 4D18 Bethesda, MD. 20892 flalonde@nih.gov
Not sure. Can you tar up the subject and send me the file here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming? Let me know when it is transferred.
On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote:
External Email - Use Caution
Hi,
We collected an MP-RAGE scan at .6mm isotropic resolution with the TR bumped up to TR=5. Subject motion artifacts were mitigated by using a KinetiCor motion correction system. We followed the recommendations for processing submillimeter scans described in the FreeSurfer Wiki i.e. we added the -cm flag to recon-all and included the mris_inflate -n 100 expert option. The attached PDF of the white matter surfaces shows that they appear to be underestimated. The surface estimates fall short of the actual grey/white matter boundary. Arrows point to the most affected areas and the second image is the same as the first but without the yellow white matter surface line. FTP is disabled on my government computer. Please specify the recipient email if I have to transfer the file using FileDrop. Could you suggest other options either at the time of scanning or in running recon-all that could help better segment the white matter?
Thanks,
François Lalonde, Ph.D.
DNU/HGB/NIMH/NIH
10 Center Drive, Room 4D18
Bethesda, MD. 20892
flalonde@nih.gov
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug
Thanks for the link but it won't let me transfer the file. I tried FileDrop but it requires an nmr.mgh.harvard.edu account and told me that user dgreve is not valid.
Sorry for the hassle.
François
On 1/22/19, 1:00 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
Not sure. Can you tar up the subject and send me the file here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming? Let me know when it is transferred.
On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > External Email - Use Caution > > Hi, > > We collected an MP-RAGE scan at .6mm isotropic resolution with the TR > bumped up to TR=5. Subject motion artifacts were mitigated by using a > KinetiCor motion correction system. We followed the recommendations > for processing submillimeter scans described in the FreeSurfer Wiki > i.e. we added the -cm flag to recon-all and included the mris_inflate > -n 100 expert option. The attached PDF of the white matter surfaces > shows that they appear to be underestimated. The surface estimates > fall short of the actual grey/white matter boundary. Arrows point to > the most affected areas and the second image is the same as the first > but without the yellow white matter surface line. FTP is disabled on > my government computer. Please specify the recipient email if I have > to transfer the file using FileDrop. Could you suggest other options > either at the time of scanning or in running recon-all that could help > better segment the white matter? > > Thanks, > > François Lalonde, Ph.D. > > DNU/HGB/NIMH/NIH > > 10 Center Drive, Room 4D18 > > Bethesda, MD. 20892 > > flalonde@nih.gov > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Use greve@nmr.mgh.harvard.edu
On 1/22/19 1:19 PM, Lalonde, Francois (NIH/NIMH) [E] wrote:
External Email - Use CautionHi Doug
Thanks for the link but it won't let me transfer the file. I tried FileDrop but it requires an nmr.mgh.harvard.edu account and told me that user dgreve is not valid.
Sorry for the hassle.
François
On 1/22/19, 1:00 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
Not sure. Can you tar up the subject and send me the file here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming? Let me know when it is transferred. On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > External Email - Use Caution > > Hi, > > We collected an MP-RAGE scan at .6mm isotropic resolution with the TR > bumped up to TR=5. Subject motion artifacts were mitigated by using a > KinetiCor motion correction system. We followed the recommendations > for processing submillimeter scans described in the FreeSurfer Wiki > i.e. we added the -cm flag to recon-all and included the mris_inflate > -n 100 expert option. The attached PDF of the white matter surfaces > shows that they appear to be underestimated. The surface estimates > fall short of the actual grey/white matter boundary. Arrows point to > the most affected areas and the second image is the same as the first > but without the yellow white matter surface line. FTP is disabled on > my government computer. Please specify the recipient email if I have > to transfer the file using FileDrop. Could you suggest other options > either at the time of scanning or in running recon-all that could help > better segment the white matter? > > Thanks, > > François Lalonde, Ph.D. > > DNU/HGB/NIMH/NIH > > 10 Center Drive, Room 4D18 > > Bethesda, MD. 20892 > > flalonde@nih.gov > > > _______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Version 6 does not work very well with such high-res data. I created a patch for the HCP that you can download from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp This works in version 6. Just follow the instructions in the README.
I ran it on your data, and it looks pretty good.
On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote:
External Email - Use Caution
Hi,
We collected an MP-RAGE scan at .6mm isotropic resolution with the TR bumped up to TR=5. Subject motion artifacts were mitigated by using a KinetiCor motion correction system. We followed the recommendations for processing submillimeter scans described in the FreeSurfer Wiki i.e. we added the -cm flag to recon-all and included the mris_inflate -n 100 expert option. The attached PDF of the white matter surfaces shows that they appear to be underestimated. The surface estimates fall short of the actual grey/white matter boundary. Arrows point to the most affected areas and the second image is the same as the first but without the yellow white matter surface line. FTP is disabled on my government computer. Please specify the recipient email if I have to transfer the file using FileDrop. Could you suggest other options either at the time of scanning or in running recon-all that could help better segment the white matter?
Thanks,
François Lalonde, Ph.D.
DNU/HGB/NIMH/NIH
10 Center Drive, Room 4D18
Bethesda, MD. 20892
flalonde@nih.gov
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug,
The data I sent was generated using the development version, freesurfer-linux-centos7_x86_64-dev-20180807-df586ca. I downloaded the patch and will rerun the scans using version 6.
Thanks, François
On 1/24/19, 3:40 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
Version 6 does not work very well with such high-res data. I created a patch for the HCP that you can download from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp This works in version 6. Just follow the instructions in the README.
I ran it on your data, and it looks pretty good.
On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > External Email - Use Caution > > Hi, > > We collected an MP-RAGE scan at .6mm isotropic resolution with the TR > bumped up to TR=5. Subject motion artifacts were mitigated by using a > KinetiCor motion correction system. We followed the recommendations > for processing submillimeter scans described in the FreeSurfer Wiki > i.e. we added the -cm flag to recon-all and included the mris_inflate > -n 100 expert option. The attached PDF of the white matter surfaces > shows that they appear to be underestimated. The surface estimates > fall short of the actual grey/white matter boundary. Arrows point to > the most affected areas and the second image is the same as the first > but without the yellow white matter surface line. FTP is disabled on > my government computer. Please specify the recipient email if I have > to transfer the file using FileDrop. Could you suggest other options > either at the time of scanning or in running recon-all that could help > better segment the white matter? > > Thanks, > > François Lalonde, Ph.D. > > DNU/HGB/NIMH/NIH > > 10 Center Drive, Room 4D18 > > Bethesda, MD. 20892 > > flalonde@nih.gov > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The dev version has the same problem :(
On 1/24/19 6:37 PM, Lalonde, Francois (NIH/NIMH) [E] wrote:
External Email - Use CautionHi Doug,
The data I sent was generated using the development version, freesurfer-linux-centos7_x86_64-dev-20180807-df586ca. I downloaded the patch and will rerun the scans using version 6.
Thanks, François
On 1/24/19, 3:40 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
Version 6 does not work very well with such high-res data. I created a patch for the HCP that you can download from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp This works in version 6. Just follow the instructions in the README. I ran it on your data, and it looks pretty good. On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > External Email - Use Caution > > Hi, > > We collected an MP-RAGE scan at .6mm isotropic resolution with the TR > bumped up to TR=5. Subject motion artifacts were mitigated by using a > KinetiCor motion correction system. We followed the recommendations > for processing submillimeter scans described in the FreeSurfer Wiki > i.e. we added the -cm flag to recon-all and included the mris_inflate > -n 100 expert option. The attached PDF of the white matter surfaces > shows that they appear to be underestimated. The surface estimates > fall short of the actual grey/white matter boundary. Arrows point to > the most affected areas and the second image is the same as the first > but without the yellow white matter surface line. FTP is disabled on > my government computer. Please specify the recipient email if I have > to transfer the file using FileDrop. Could you suggest other options > either at the time of scanning or in running recon-all that could help > better segment the white matter? > > Thanks, > > François Lalonde, Ph.D. > > DNU/HGB/NIMH/NIH > > 10 Center Drive, Room 4D18 > > Bethesda, MD. 20892 > > flalonde@nih.gov > > > _______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug,
Sorry for the delay in getting back to you. I wanted feedback from the other members of the studies. We all agree that the patch worked wonderfully.
Thanks! François
On 1/24/19, 7:34 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
The dev version has the same problem :(
On 1/24/19 6:37 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > External Email - Use Caution > > Hi Doug, > > The data I sent was generated using the development version, freesurfer-linux-centos7_x86_64-dev-20180807-df586ca. I downloaded the patch and will rerun the scans using version 6. > > Thanks, > François > > > On 1/24/19, 3:40 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote: > > Version 6 does not work very well with such high-res data. I created a > patch for the HCP that you can download from here > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp > This works in version 6. Just follow the instructions in the README. > > I ran it on your data, and it looks pretty good. > > > On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > > > External Email - Use Caution > > > > Hi, > > > > We collected an MP-RAGE scan at .6mm isotropic resolution with the TR > > bumped up to TR=5. Subject motion artifacts were mitigated by using a > > KinetiCor motion correction system. We followed the recommendations > > for processing submillimeter scans described in the FreeSurfer Wiki > > i.e. we added the -cm flag to recon-all and included the mris_inflate > > -n 100 expert option. The attached PDF of the white matter surfaces > > shows that they appear to be underestimated. The surface estimates > > fall short of the actual grey/white matter boundary. Arrows point to > > the most affected areas and the second image is the same as the first > > but without the yellow white matter surface line. FTP is disabled on > > my government computer. Please specify the recipient email if I have > > to transfer the file using FileDrop. Could you suggest other options > > either at the time of scanning or in running recon-all that could help > > better segment the white matter? > > > > Thanks, > > > > François Lalonde, Ph.D. > > > > DNU/HGB/NIMH/NIH > > > > 10 Center Drive, Room 4D18 > > > > Bethesda, MD. 20892 > > > > flalonde@nih.gov > > > > > > _______________________________________________ > > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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good to hear!
On 2/5/19 12:19 PM, Lalonde, Francois (NIH/NIMH) [E] wrote:
External Email - Use CautionHi Doug,
Sorry for the delay in getting back to you. I wanted feedback from the other members of the studies. We all agree that the patch worked wonderfully.
Thanks! François
On 1/24/19, 7:34 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
The dev version has the same problem :( On 1/24/19 6:37 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > External Email - Use Caution > > Hi Doug, > > The data I sent was generated using the development version, freesurfer-linux-centos7_x86_64-dev-20180807-df586ca. I downloaded the patch and will rerun the scans using version 6. > > Thanks, > François > > > On 1/24/19, 3:40 PM, "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> wrote: > > Version 6 does not work very well with such high-res data. I created a > patch for the HCP that you can download from here > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp > This works in version 6. Just follow the instructions in the README. > > I ran it on your data, and it looks pretty good. > > > On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > > > External Email - Use Caution > > > > Hi, > > > > We collected an MP-RAGE scan at .6mm isotropic resolution with the TR > > bumped up to TR=5. Subject motion artifacts were mitigated by using a > > KinetiCor motion correction system. We followed the recommendations > > for processing submillimeter scans described in the FreeSurfer Wiki > > i.e. we added the -cm flag to recon-all and included the mris_inflate > > -n 100 expert option. The attached PDF of the white matter surfaces > > shows that they appear to be underestimated. The surface estimates > > fall short of the actual grey/white matter boundary. Arrows point to > > the most affected areas and the second image is the same as the first > > but without the yellow white matter surface line. FTP is disabled on > > my government computer. Please specify the recipient email if I have > > to transfer the file using FileDrop. Could you suggest other options > > either at the time of scanning or in running recon-all that could help > > better segment the white matter? > > > > Thanks, > > > > François Lalonde, Ph.D. > > > > DNU/HGB/NIMH/NIH > > > > 10 Center Drive, Room 4D18 > > > > Bethesda, MD. 20892 > > > > flalonde@nih.gov > > > > > > _______________________________________________ > > 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 > > > _______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Doug,
I just want to verify that I'm using the patch for high resolution scans properly. We noticed that the output of "recon-all.v6.hires -conf2hires" has many volumes with 1 mm isotropic voxels. The only volumes with the original resolution ( 0.6 mm) are rawavg.aseg.presurf.mgz, rawavg.brain.finalsurfs.mgz, rawavg.brain.fs.mgz, rawavg.cmdc0.mgz, rawavg.cmdc.mgz, rawavg.filled.mgz, rawavg.mgz, rawavg.norm.mgz, and rawavg.wm.mgz. So, the surfaces are processed at the higher resolution but other steps require resampling to 1 mm isotropic. We can still display the results at higher resolution in freeview by using one of the hires volumes like rawavg.brain.fs.mgz on which to overlay the higher resolution surfaces. Subcortical segmentations and cortical parcellations are done at 1 mm isotropic resolution. Is this correct?
Thanks, François
On 2/5/19, 12:41 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote:
good to hear!
On 2/5/19 12:19 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > External Email - Use Caution > > Hi Doug, > > Sorry for the delay in getting back to you. I wanted feedback from the other members of the studies. We all agree that the patch worked wonderfully. > > Thanks! > François > > > On 1/24/19, 7:34 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote: > > The dev version has the same problem :( > > On 1/24/19 6:37 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > External Email - Use Caution > > > > Hi Doug, > > > > The data I sent was generated using the development version, freesurfer-linux-centos7_x86_64-dev-20180807-df586ca. I downloaded the patch and will rerun the scans using version 6. > > > > Thanks, > > François > > > > > > On 1/24/19, 3:40 PM, "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu wrote: > > > > Version 6 does not work very well with such high-res data. I created a > > patch for the HCP that you can download from here > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp > > This works in version 6. Just follow the instructions in the README. > > > > I ran it on your data, and it looks pretty good. > > > > > > On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > > > > > External Email - Use Caution > > > > > > Hi, > > > > > > We collected an MP-RAGE scan at .6mm isotropic resolution with the TR > > > bumped up to TR=5. Subject motion artifacts were mitigated by using a > > > KinetiCor motion correction system. We followed the recommendations > > > for processing submillimeter scans described in the FreeSurfer Wiki > > > i.e. we added the -cm flag to recon-all and included the mris_inflate > > > -n 100 expert option. The attached PDF of the white matter surfaces > > > shows that they appear to be underestimated. The surface estimates > > > fall short of the actual grey/white matter boundary. Arrows point to > > > the most affected areas and the second image is the same as the first > > > but without the yellow white matter surface line. FTP is disabled on > > > my government computer. Please specify the recipient email if I have > > > to transfer the file using FileDrop. Could you suggest other options > > > either at the time of scanning or in running recon-all that could help > > > better segment the white matter? > > > > > > Thanks, > > > > > > François Lalonde, Ph.D. > > > > > > DNU/HGB/NIMH/NIH > > > > > > 10 Center Drive, Room 4D18 > > > > > > Bethesda, MD. 20892 > > > > > > flalonde@nih.gov > > > > > > > > > _______________________________________________ > > > 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 > > > > > > _______________________________________________ > > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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Greve, Douglas N.,Ph.D. -
Lalonde, Francois (NIH/NIMH) [E]