External Email - Use Caution Hello Bruce,
I haven't heard back from you so I just wanted to follow up and ask if you had the chance to look at the data that I uploaded. Cheers Carolin On Mon, Mar 29, 2021 at 4:01 PM Caroline Chwiesko <cchwi...@uci.edu> wrote: > Because the dataset is already uploaded would it be possible to also look > at the following in this dataset?: > > For editing of the subcortical segmentation in the aparc+aseg file, there > is a spot where I can not figure out if this structure is supposed to be > part of the caudate or the choroid plexus. In most of my subjects it is > segmented as caudate but based on the shape I don t think that this is > correct. I am wondering if there is somewhere a dataset that we can > download and that displays an optimal/correct segmentation of the > subcortical structures to serve as a guide for editing? > > The coordinates for the location I am not sure about are: > for right :RAS 8.24 10.85 33.75, in the aparc+aseg file its 118 124 144 > for left: RAS -12.76 14.71 29.46, in the aparc+aseg file its 139 128 148 > > Thank you very much in advance for your help! > Carolin > > On Mon, Mar 29, 2021 at 3:32 PM Caroline Chwiesko <cchwi...@uci.edu> > wrote: > >> RAS: 6.11, 57.54, 60.36 >> brainmask [120, 98, 191] >> Talairach 115.59, 127.61, 202.35 >> >> On Mon, Mar 29, 2021 at 3:08 PM Fischl, Bruce <bfis...@mgh.harvard.edu> >> wrote: >> >>> Thanks. What are the voxel coords of the location you wanted us to take >>> a look at? >>> >>> >>> >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko >>> *Sent:* Monday, March 29, 2021 5:54 PM >>> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> *Subject:* Re: [Freesurfer] How to edit GM when WM is ok >>> >>> >>> >>> * External Email - Use Caution * >>> >>> Hello Bruce, >>> >>> >>> >>> i don t have a good understanding of how the upload works so i just >>> called those files img1.png, img2.png and img3.png thinking that you will >>> be able to connect those files with my email address. I uploaded now the >>> entire zipped subject directory. This file is called carolinechwiesko.zip. >>> It includes also a directory called images which includes images of the >>> problematic spot in all 3 orientations. >>> >>> >>> >>> I got the following output in the terminal while uploading my file. I >>> hope that this means that the upload was successful: >>> >>> 230 Login successful. >>> >>> Remote system type is UNIX. >>> >>> Using binary mode to transfer files. >>> >>> ftp> cd transfer/incoming >>> >>> 250 Directory successfully changed. >>> >>> ftp> put carolinechwiesko.zip >>> >>> local: carolinechwiesko.zip remote: carolinechwiesko.zip >>> >>> 200 PORT command successful. Consider using PASV. >>> >>> 150 Ok to send data. >>> >>> >>> >>> Again thank you very much for your help with this! >>> >>> Cheers >>> >>> Carolin >>> >>> >>> >>> >>> >>> >>> >>> On Sat, Mar 27, 2021 at 8:35 AM Fischl, Bruce <bfis...@mgh.harvard.edu> >>> wrote: >>> >>> Hi Carolin >>> >>> >>> >>> What did you name them? Also, we won’t really be able to diagnose things >>> unless you upload the entire tarred/gzipped subject directory >>> >>> >>> >>> Cheers >>> >>> Bruce >>> >>> >>> >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko >>> *Sent:* Friday, March 26, 2021 8:04 PM >>> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> *Subject:* Re: [Freesurfer] How to edit GM when WM is ok >>> >>> >>> >>> * External Email - Use Caution * >>> >>> Thank you for your response! I followed the instructions for FTP file >>> exchange. And did then: >>> >>> >>> >>> ftp> cd transfer/incoming >>> >>> ftp> put filename.txt >>> >>> >>> >>> Are the images not there? >>> >>> Cheers >>> >>> Carolin >>> >>> >>> >>> On Fri, Mar 26, 2021 at 3:20 PM Fischl, Bruce <bfis...@mgh.harvard.edu> >>> wrote: >>> >>> Hi Carolin >>> >>> >>> >>> Where did you upload the images? >>> Bruce >>> >>> >>> >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko >>> *Sent:* Friday, March 26, 2021 6:08 PM >>> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> *Subject:* Re: [Freesurfer] How to edit GM when WM is ok >>> >>> >>> >>> * External Email - Use Caution * >>> >>> Hello Bruce, >>> >>> I wrote a week ago to this mailing list to ask for advice about how to >>> edit an issue where an entire Gyrus will not be captured by the pial >>> surface. I uploaded some images to show what that looks like. I just wanted >>> to send a friendly reminder to make sure it won't be forgotten ;) >>> >>> Thank you very much for any help! >>> >>> >>> >>> Cheers >>> >>> Carolin >>> >>> >>> >>> On Fri, Mar 19, 2021 at 4:54 PM Caroline Chwiesko <cchwi...@uci.edu> >>> wrote: >>> >>> Hi Bruce, >>> >>> thank you very much for taking a look at that. I uploaded 3 images in >>> different orientations. I can not see any white matter. >>> >>> >>> >>> Cheers >>> >>> Carolin >>> >>> >>> >>> >>> >>> On Fri, Mar 19, 2021 at 7:26 AM Fischl, Bruce <bfis...@mgh.harvard.edu> >>> wrote: >>> >>> Hi Carolin >>> >>> >>> >>> Yes, I guess send along images using all 3 orientations. There has to be >>> some white matter there somewhere…. >>> >>> Cheers >>> >>> Bruce >>> >>> >>> >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Caroline Chwiesko >>> *Sent:* Friday, March 19, 2021 12:28 AM >>> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> *Subject:* [Freesurfer] How to edit GM when WM is ok >>> >>> >>> >>> * External Email - Use Caution * >>> >>> Hello Freesurfer experts, >>> >>> >>> >>> i am doing some editing after recon-all. I have the issue that one gyrus >>> is not captured by the pial surface. There is no wm that is wrong and that >>> i could correct. It looks like this gyrus has a weird angle so there is >>> actually no WM visible. How can such an error be corrected? I am happy to >>> send a couple images if needed. >>> >>> >>> >>> Thank you very much in advance for any help! >>> >>> Cheers >>> >>> Carolin >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/16tQ_T6VRny_u0gIXHY4RtleputhqLXJHoXnjyVKOeH91-3ukwmUhjSHULP46IbsfyTsW0tTVcxSs6DXLcG4YtrScWs5lRot9hjPXY-25uhebEe1kSy0RVd58l5VCMKJ9gzro4K_9ijN26xtcURw4gv8UoYVwcaocXQdKMrDS_wXR83Nqe22Q5XhrZ0wKD4OVRWjmrYA1blG-QOXKNFSZq2_r6FzlBji6LFVBjaRPqCM1RwumxMuGpfKGQH-YNuY9z9-rlbAD87aUzDEJedN2Tw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <https://secure-web.cisco.com/1niNiJqZPAU_BwdWuyKfUgvGJumNQAo6mbJhKeNlfs_2Mh5cDQppJl75VfBAoN-1GJ7kWtojMqeH4mHdQpW-8urrYDir0w2VJlTIW_rRBQO_1BOrfNByyysdYt6w5HVkogl_nH59vslj0dkR46uyo79pfPIzjBBOTIh2w56yH-ILMNEPvd3-V6iwIHqfpO_51s3XbpUhR4-XbS66RF70eirz5HFqAMqfbsgy4EN2KyvfKXYwbicVqnp2QPZ-c89nArCB2gGomICANaSQBJA173Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/16tQ_T6VRny_u0gIXHY4RtleputhqLXJHoXnjyVKOeH91-3ukwmUhjSHULP46IbsfyTsW0tTVcxSs6DXLcG4YtrScWs5lRot9hjPXY-25uhebEe1kSy0RVd58l5VCMKJ9gzro4K_9ijN26xtcURw4gv8UoYVwcaocXQdKMrDS_wXR83Nqe22Q5XhrZ0wKD4OVRWjmrYA1blG-QOXKNFSZq2_r6FzlBji6LFVBjaRPqCM1RwumxMuGpfKGQH-YNuY9z9-rlbAD87aUzDEJedN2Tw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <https://secure-web.cisco.com/1BS8cQkF9alr23QUc2ilpru4PaiGB475uAOj-ft6bmLpuPoSRn9o7DsbKKr-eyfONzfLjhY06cQ_GpAnB7FiRN4T-y1LxaZXoAPAaOlEQRwUS1xqqtTEWyMwnO58AuRkX0kyOAZRoVzLC7EK8nIY-mIVrWJNwwD8QIkrIous5A4khjy9E9P8xLZL06wveBjyqcu2z7I6uiy52lva157F2-xrc0p9K7IWnOPkkw_QvVs9d62sGOAvLk3zf-rPEupliP3tvtZMfAXRF8OvohzOANw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/16tQ_T6VRny_u0gIXHY4RtleputhqLXJHoXnjyVKOeH91-3ukwmUhjSHULP46IbsfyTsW0tTVcxSs6DXLcG4YtrScWs5lRot9hjPXY-25uhebEe1kSy0RVd58l5VCMKJ9gzro4K_9ijN26xtcURw4gv8UoYVwcaocXQdKMrDS_wXR83Nqe22Q5XhrZ0wKD4OVRWjmrYA1blG-QOXKNFSZq2_r6FzlBji6LFVBjaRPqCM1RwumxMuGpfKGQH-YNuY9z9-rlbAD87aUzDEJedN2Tw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <https://secure-web.cisco.com/1J_oIoYOhJvnRwnRW-4mvRYHkbS5YnJ-4a7ToFYTxtnkArwteHXKuS4d4Wbv1jNBOAxWg-iEK4odlolDNbypwWrlvCH1BW_KMwQ9tHAPOKCgj4XUClFwsEmf0AR5-6yBvIMJ19n4JeUOabYx10eAx82aCv3dCpQDue-uBJz6hYzhzm3UpZWjYZUB1O0AyetRlARVuEpcPRWza5ygSj1w6L2i9jbFvdlCCfuJVUs_y-p5TjAcxJyMHLB4Es4tx8h3kS5XOIkL9CKBoeUCArT5Hkw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://secure-web.cisco.com/16tQ_T6VRny_u0gIXHY4RtleputhqLXJHoXnjyVKOeH91-3ukwmUhjSHULP46IbsfyTsW0tTVcxSs6DXLcG4YtrScWs5lRot9hjPXY-25uhebEe1kSy0RVd58l5VCMKJ9gzro4K_9ijN26xtcURw4gv8UoYVwcaocXQdKMrDS_wXR83Nqe22Q5XhrZ0wKD4OVRWjmrYA1blG-QOXKNFSZq2_r6FzlBji6LFVBjaRPqCM1RwumxMuGpfKGQH-YNuY9z9-rlbAD87aUzDEJedN2Tw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >>
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