Hi guys,
Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere.
Thanks!
Best,
Marja
Hi Marja
how did you swap them? And more importantly, how did you check that the orientations were correct after conversion?
cheers Bruce
On Mon, 13 Jun 2016, Marja Caverlé wrote:
Hi guys,
Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere.
Thanks!
Best,
Marja
Hi Bruce,
I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard).
Best,
Marja
On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Marja
how did you swap them? And more importantly, how did you check that the orientations were correct after conversion?
cheers Bruce
On Mon, 13 Jun 2016, Marja Caverlé wrote:
Hi guys,
Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere.
Thanks!
Best,
Marja
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Hi Marja
what did you visualize it in? I would suggest freeview
cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote:
Hi Bruce,
I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard).
Best,
Marja
On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja
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.
Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L.
Thanks!
On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Marja
what did you visualize it in? I would suggest freeview
cheers Bruce
On Tue, 14 Jun 2016, Marja Caverlé wrote:
Hi Bruce,
I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard).
Best,
Marja
On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Marja
how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja
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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.
so you convert from dicom to nifti, then view in freeview and you think that the anatomical orientations are incorrect? That should definitely not be the case
On Tue, 14 Jun 2016, Marja Caverlé wrote:
Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L.
Thanks!
On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
what did you visualize it in? I would suggest freeview cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard). Best, Marja On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja _______________________________________________ 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.
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No, when I view them in freeview the orientation is the same as in the original dicoms, but the results in the .stats files made me think that left and right might be swapped. Of course this could just really be the results of the correct hemispheres, but that is why I asked whether you are aware of any dimension switching during the recon-all. If not, than I can safely assume that the results are correct.
Best,
Marja
On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
so you convert from dicom to nifti, then view in freeview and you think that the anatomical orientations are incorrect? That should definitely not be the case
On Tue, 14 Jun 2016, Marja Caverlé wrote:
Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer
and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L.
Thanks!
On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Marja
what did you visualize it in? I would suggest freeview cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard). Best, Marja On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja _______________________________________________ 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.
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Hi Marja
why are you converting at all? Why not just give one of the dicom files in the correct series to recon-all directly? I don't think we've ever seen an orientation problem if you process that way cheers Bruce
On Tue, 14 Jun 2016, Marja Caverlé wrote:
No, when I view them in freeview the orientation is the same as in the original dicoms, but the results in the .stats files made me think that left and right might be swapped. Of course this could just really be the results of the correct hemispheres, but that is why I asked whether you are aware of any dimension switching during the recon-all. If not, than I can safely assume that the results are correct.
Best,
Marja
On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: so you convert from dicom to nifti, then view in freeview and you think that the anatomical orientations are incorrect? That should definitely not be the case
On Tue, 14 Jun 2016, Marja Caverlé wrote: Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L. Thanks! On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja what did you visualize it in? I would suggest freeview cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard). Best, Marja On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja _______________________________________________ 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 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.
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Hi Bruce,
I converted first of all because freesurfer did not accept the dicom files. Furthermore the dicom's consist of a lot of files of different scans, and they are not named accordingly. The whole folder consists of files called eg 1254890234, so I have no clue how to get the right files.
Thanks!
On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Marja
why are you converting at all? Why not just give one of the dicom files in the correct series to recon-all directly? I don't think we've ever seen an orientation problem if you process that way
cheers Bruce
On Tue, 14 Jun 2016, Marja Caverlé wrote:
No, when I view them in freeview the orientation is the same as in the
original dicoms, but the results in the .stats files made me think that left and right might be swapped. Of course this could just really be the results of the correct hemispheres, but that is why I asked whether you are aware of any dimension switching during the recon-all. If not, than I can safely assume that the results are correct.
Best,
Marja
On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: so you convert from dicom to nifti, then view in freeview and you think that the anatomical orientations are incorrect? That should definitely not be the case
On Tue, 14 Jun 2016, Marja Caverlé wrote: Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L. Thanks! On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja what did you visualize it in? I would suggest freeview cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard). Best, Marja On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja _______________________________________________ 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 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.
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What do you mean that FS did not accept the dicom files? Can you provide a command line and terminal output? You can use dcmunpack -src /path/to/dicom to get a list of the series in a dicom folder
On 6/13/16 9:57 PM, Marja Caverlé wrote:
Hi Bruce,
I converted first of all because freesurfer did not accept the dicom files. Furthermore the dicom's consist of a lot of files of different scans, and they are not named accordingly. The whole folder consists of files called eg 1254890234, so I have no clue how to get the right files.
Thanks!
On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Marja why are you converting at all? Why not just give one of the dicom files in the correct series to recon-all directly? I don't think we've ever seen an orientation problem if you process that way cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: No, when I view them in freeview the orientation is the same as in the original dicoms, but the results in the .stats files made me think that left and right might be swapped. Of course this could just really be the results of the correct hemispheres, but that is why I asked whether you are aware of any dimension switching during the recon-all. If not, than I can safely assume that the results are correct. Best, Marja On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: so you convert from dicom to nifti, then view in freeview and you think that the anatomical orientations are incorrect? That should definitely not be the case On Tue, 14 Jun 2016, Marja Caverlé wrote: Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L. Thanks! On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Marja what did you visualize it in? I would suggest freeview cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard). Best, Marja On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Marja how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
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Hi Bruce,
When I wanted to view them in freeview, simply nothing happened. Freeview did not load the files, so I assumed it did not work with dicoms, that's why I converted them.
Best,
Marja
On Tue, Jun 14, 2016 at 12:23 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
What do you mean that FS did not accept the dicom files? Can you provide a command line and terminal output? You can use dcmunpack -src /path/to/dicom to get a list of the series in a dicom folder
On 6/13/16 9:57 PM, Marja Caverlé wrote:
Hi Bruce,
I converted first of all because freesurfer did not accept the dicom files. Furthermore the dicom's consist of a lot of files of different scans, and they are not named accordingly. The whole folder consists of files called eg 1254890234, so I have no clue how to get the right files.
Thanks!
On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Marja
why are you converting at all? Why not just give one of the dicom files in the correct series to recon-all directly? I don't think we've ever seen an orientation problem if you process that way
cheers Bruce
On Tue, 14 Jun 2016, Marja Caverlé wrote:
No, when I view them in freeview the orientation is the same as in the
original dicoms, but the results in the .stats files made me think that left and right might be swapped. Of course this could just really be the results of the correct hemispheres, but that is why I asked whether you are aware of any dimension switching during the recon-all. If not, than I can safely assume that the results are correct.
Best,
Marja
On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edufischl@nmr.mgh.harvard.edu> wrote: so you convert from dicom to nifti, then view in freeview and you think that the anatomical orientations are incorrect? That should definitely not be the case
On Tue, 14 Jun 2016, Marja Caverlé wrote: Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L. Thanks! On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja what did you visualize it in? I would suggest freeview cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard). Best, Marja On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja _______________________________________________ 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 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.
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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
freeview works fine with most dicoms. Do you get an error message? On Tue, 14 Jun 2016, Marja Caverlé wrote:
Hi Bruce,
When I wanted to view them in freeview, simply nothing happened. Freeview did not load the files, so I assumed it did not work with dicoms, that's why I converted them.
Best,
Marja
On Tue, Jun 14, 2016 at 12:23 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote: What do you mean that FS did not accept the dicom files? Can you provide a command line and terminal output? You can use dcmunpack -src /path/to/dicom to get a list of the series in a dicom folder
On 6/13/16 9:57 PM, Marja Caverlé wrote: Hi Bruce, I converted first of all because freesurfer did not accept the dicom files. Furthermore the dicom's consist of a lot of files of different scans, and they are not named accordingly. The whole folder consists of files called eg 1254890234, so I have no clue how to get the right files. Thanks!On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
why are you converting at all? Why not just give one of the dicom files in the correct series to recon-all directly? I don't think we've ever seen an orientation problem if you process that way cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: No, when I view them in freeview the orientation is the same as in the original dicoms, but the results in the .stats files made me think that left and right might be swapped. Of course this could just really be the results of the correct hemispheres, but that is why I asked whether you are aware of any dimension switching during the recon-all. If not, than I can safely assume that the results are correct. Best, Marja On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: so you convert from dicom to nifti, then view in freeview and you think that the anatomical orientations are incorrect? That should definitely not be the case On Tue, 14 Jun 2016, Marja Caverlé wrote: Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L. Thanks! On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja what did you visualize it in? I would suggest freeview cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard). Best, Marja On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja _______________________________________________ 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 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 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.
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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.
Hi Bruce,
I did not get any error message, the page just remained empty after selecting the files. Maybe my files were the reason why it didn't work.
Best,
Marja
On Tue, Jun 14, 2016 at 10:50 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
freeview works fine with most dicoms. Do you get an error message?
On Tue, 14 Jun 2016, Marja Caverlé wrote:
Hi Bruce,
When I wanted to view them in freeview, simply nothing happened. Freeview did not load the files, so I assumed it did not work with dicoms, that's why I converted them.
Best,
Marja
On Tue, Jun 14, 2016 at 12:23 PM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote: What do you mean that FS did not accept the dicom files? Can you provide a command line and terminal output? You can use dcmunpack -src /path/to/dicom to get a list of the series in a dicom folder
On 6/13/16 9:57 PM, Marja Caverlé wrote: Hi Bruce, I converted first of all because freesurfer did not accept the dicom files. Furthermore the dicom's consist of a lot of files of different scans, and they are not named accordingly. The whole folder consists of files called eg 1254890234, so I have no clue how to get the right files. Thanks!On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
why are you converting at all? Why not just give one of the dicom files in the correct series to recon-all directly? I don't think we've ever seen an orientation problem if you process that way cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: No, when I view them in freeview the orientation is the same as in the original dicoms, but the results in the .stats files made me think that left and right might be swapped. Of course this could just really be the results of the correct hemispheres, but that is why I asked whether you are aware of any dimension switching during the recon-all. If not, than I can safely assume that the results are correct. Best, Marja On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: so you convert from dicom to nifti, then view in freeview and you think that the anatomical orientations are incorrect? That should definitely not be the case On Tue, 14 Jun 2016, Marja Caverlé wrote: Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L. Thanks! On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja what did you visualize it in? I would suggest freeview cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard). Best, Marja On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja _______________________________________________ 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 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 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.
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Would it be possible to send us a file?
Best, Ruopeng
On Jun 14, 2016, at 8:52 AM, Marja Caverlé marja.caverle@gmail.com wrote:
Hi Bruce,
I did not get any error message, the page just remained empty after selecting the files. Maybe my files were the reason why it didn't work.
Best,
Marja
On Tue, Jun 14, 2016 at 10:50 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: freeview works fine with most dicoms. Do you get an error message?
On Tue, 14 Jun 2016, Marja Caverlé wrote:
Hi Bruce,
When I wanted to view them in freeview, simply nothing happened. Freeview did not load the files, so I assumed it did not work with dicoms, that's why I converted them.
Best,
Marja
On Tue, Jun 14, 2016 at 12:23 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote: What do you mean that FS did not accept the dicom files? Can you provide a command line and terminal output? You can use dcmunpack -src /path/to/dicom to get a list of the series in a dicom folder
On 6/13/16 9:57 PM, Marja Caverlé wrote: Hi Bruce, I converted first of all because freesurfer did not accept the dicom files. Furthermore the dicom's consist of a lot of files of different scans, and they are not named accordingly. The whole folder consists of files called eg 1254890234, so I have no clue how to get the right files. Thanks!On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Marja
why are you converting at all? Why not just give one of the dicom files in the correct series to recon-all directly? I don't think we've ever seen an orientation problem if you process that way cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: No, when I view them in freeview the orientation is the same as in the original dicoms, but the results in the .stats files made me think that left and right might be swapped. Of course this could just really be the results of the correct hemispheres, but that is why I asked whether you are aware of any dimension switching during the recon-all. If not, than I can safely assume that the results are correct. Best, Marja On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: so you convert from dicom to nifti, then view in freeview and you think that the anatomical orientations are incorrect? That should definitely not be the case On Tue, 14 Jun 2016, Marja Caverlé wrote: Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L. Thanks! On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Marja what did you visualize it in? I would suggest freeview cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard). Best, Marja On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Marja how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.
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Hi Ruopeng,
I am very sorry since I think you would like to figure out why freeview did not take my DICOM's, but due to privacy issues I have deleted the DICOM's after the recon -all (on the niftis) was completed without any errors. Basically when I selected the files, nothing happened, while when I selected the nifti it loaded the scan. No error or anything like that.
Best,
Marja
On Tue, Jun 14, 2016 at 11:51 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
Would it be possible to send us a file?
Best, Ruopeng
On Jun 14, 2016, at 8:52 AM, Marja Caverlé marja.caverle@gmail.com wrote:
Hi Bruce,
I did not get any error message, the page just remained empty after selecting the files. Maybe my files were the reason why it didn't work.
Best,
Marja
On Tue, Jun 14, 2016 at 10:50 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
freeview works fine with most dicoms. Do you get an error message?
On Tue, 14 Jun 2016, Marja Caverlé wrote:
Hi Bruce,
When I wanted to view them in freeview, simply nothing happened. Freeview did not load the files, so I assumed it did not work with dicoms, that's why I converted them.
Best,
Marja
On Tue, Jun 14, 2016 at 12:23 PM, Douglas Greve < greve@nmr.mgh.harvard.edu> wrote: What do you mean that FS did not accept the dicom files? Can you provide a command line and terminal output? You can use dcmunpack -src /path/to/dicom to get a list of the series in a dicom folder
On 6/13/16 9:57 PM, Marja Caverlé wrote: Hi Bruce, I converted first of all because freesurfer did not accept the dicom files. Furthermore the dicom's consist of a lot of files of different scans, and they are not named accordingly. The whole folder consists of files called eg 1254890234, so I have no clue how to get the right files. Thanks!On Tue, Jun 14, 2016 at 5:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja
why are you converting at all? Why not just give one of the dicom files in the correct series to recon-all directly? I don't think we've ever seen an orientation problem if you process that way cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: No, when I view them in freeview the orientation is the same as in the original dicoms, but the results in the .stats files made me think that left and right might be swapped. Of course this could just really be the results of the correct hemispheres, but that is why I asked whether you are aware of any dimension switching during the recon-all. If not, than I can safely assume that the results are correct. Best, Marja On Tue, Jun 14, 2016 at 1:29 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: so you convert from dicom to nifti, then view in freeview and you think that the anatomical orientations are incorrect? That should definitely not be the case On Tue, 14 Jun 2016, Marja Caverlé wrote: Well the DICOMs I visualized in osiriX, and the niftis in both freesurfer and fsl. And there they seemed to match. So my question is; is there a possibility that dimensions are swapped during the recon -all? If not, then I am sure R=R and L=L. Thanks! On Tue, Jun 14, 2016 at 12:55 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja what did you visualize it in? I would suggest freeview cheers Bruce On Tue, 14 Jun 2016, Marja Caverlé wrote: Hi Bruce, I converted the images with MRIconvert, then I swapped them in FSL with swapdim. I checked the images by opening the original dicoms and the converted niftis, and then visually compared them (since the heads are not very symmetrical that was not too hard). Best, Marja On Tue, Jun 14, 2016 at 12:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Marja how did you swap them? And more importantly, how did you check that the orientations were correct after conversion? cheers Bruce On Mon, 13 Jun 2016, Marja Caverlé wrote: Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja _______________________________________________ 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 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 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.
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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.
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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.
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Bruce Fischl -
Douglas Greve -
Marja Caverlé -
Ruopeng Wang