[Freesurfer] sulcus in the orbitofrontal wm
Dear list: We are editing wm and facing a problem we do not know how to solve. In the orbitofrontal wm there is a sulcus that has been fully included into the wm boundary. However there is not wm mask to be erased. I have uploaded the file 40_001 and I would be grateful if could take a look. This problem is located on coordinates Talairach (wm) 110.66, 158.70, 165.37 In addition, there is an hyperintensity in the extreme of the orbitofrontal wm we would like you to take a look and work out the best solution (I gess control points would fix it?) This is on coordinates 111.29, 161.59, 178.55. Thanks in advance -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n* *39011 Santander, Spain* ___ 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] Fwd: wm topological defects
To illustrate the previous case here there is an image in which there is a discrepancy between the wm surface and the smoothwm.nofix. Is it necessary to fix it or not? Thanks -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n* *39011 Santander, Spain* -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n* *39011 Santander, Spain* ___ 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] wm topological defects
Dear all: Regarding wm edits, it is shown in the tutorial how to proceed with "holes" that appear in the smoothwm.nofix. However, those holes do not necessarily affect the wm matter surface. So is it recommendable to check if holes in the smoothwm.nofix surface affect the real wm surface before correcting them? And, what is the purpose of the smoothwm.nofix, is it used for other issues? Thank you -- *Manuel Delgado Alvarado, MD* *Predoctoral Researcher* *Neuroimaging Unit, IDIVAL* *Avda. Cardenal Herrera Oria s/n* *39011 Santander, Spain* ___ 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.
Re: [Freesurfer] Outputs from 5.3 to 6.0
Thank you very mucho for your help 2017-06-09 18:27 GMT+02:00 Antonin Skoch <a...@ikem.cz>: > Dear Manuel, > > I would chime in with my current experience with transfering v5.3 > reconstructions to v6.0: The wm segmentation results (and therefore > white/pial surfaces, apart from other things) are different between > versions, especially in ambiguous areas and especially if there is a > difference in interpolation during conform step (in v 6.0 the cubic > interpolation is off; if it is off or on in v5.3 it depends on whether you > used patched version of recon-all or not). It of course also depends on the > quality of your data. > > In any case, my experience is, if you want to keep high quality of your > results, you probably would need to re-inspect your data again and correct > newly appeared errors in surfaces. > > Antonin Skoch > > all the edits will be taken into account regardless of what command line args > you use > > On 6/9/17 3:08 AM, Manuel Delgado wrote: > > Dear all, > > > Regarding this issue: http://www.mail-archive.com/ > freesurfer@nmr.mgh.harvard.edu/msg51931.html we have the same situation. > We are going to reprocess data previously processed with FS 5.3. If we > proceed with *recon-all -all *will all the edits be taken into account > (i.e. skull strip, control points, wm and pial edits) or is it necessary > to proceed with ordered steps (i.e -autorecon-pial, then -autorecon2-cp > autorecon3, and so on)? > > Thanks in advance, > > Manuel > > > > ___ > 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. > > -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ 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] Outputs from 5.3 to 6.0
Dear all, Regarding this issue: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51931.html we have the same situation. We are going to reprocess data previously processed with FS 5.3. If we proceed with *recon-all -all *will all the edits be taken into account (i.e. skull strip, control points, wm and pial edits) or is it necessary to proceed with ordered steps (i.e -autorecon-pial, then -autorecon2-cp autorecon3, and so on)? Thanks in advance, Manuel -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ 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] Longitudinal hippocampal subfields analysis
Dear all, I set out to perform a longitudinal analysis of hippocampal subfields. I have already edited the cross and/or the bases when necessary and obtained the longs. Then I have obtained the hippocampal subfields by the automated pipeline: recon-all -s -hippocampal-subfields-T1. Now I am going to create the qdec table to proceed with the analysis, but I don't know whether I have to smooth the data by recon-all -long -qcahe before the analysis, or given that hippocampal subregions have been extracted by using its own pipeline it is not necessary to do any smoothing. Thanks -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ 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.
Re: [Freesurfer] Recon-all after edits
Thank you Bruce. However, doing the recon-all for both the wm and the cp will have the same result as adding the control points and recon-all in a first step, and then doing the wm edits and recon-all again? I think that if you perform the wm edits in the result of having added the cp, the edits you need may be different than if you have not done the cp step previously. Is this right? Thus, even though it is possible to do an only recon-all step for both edits, is it recommendable to do it? On 30/03/17 15:51, Bruce Fischl wrote: Hi Manuel -autorecon2-cp runs all the steps that autorecon2-wm does so it is redundant. If you run autorecon2-cp and autorecon3 you will get everything (unless you edit the aseg) cheers Bruce On Thu, 30 Mar 2017, Manuel Delgado wrote: Dear list, There is an issue that I have been concerned about since the beginning of my FS learning, as I have found somehow contradictory information in the tutorials. Is there a way to do an only recon-all after all the edits have been made to a subject? For example, if you have edited all the possible steps (skullstrip, control points, wm and pial surface) is it possible to use all the flags for each step in one only step? Something like: recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid Or on the other hand each step needs its own recon-all with its appropriate flag? Thank you -- Manuel Delgado Alvarado, MD Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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] Recon-all after edits
Dear list, There is an issue that I have been concerned about since the beginning of my FS learning, as I have found somehow contradictory information in the tutorials. Is there a way to do an only recon-all after all the edits have been made to a subject? For example, if you have edited all the possible steps (skullstrip, control points, wm and pial surface) is it possible to use all the flags for each step in one only step? Something like: recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid Or on the other hand each step needs its own recon-all with its appropriate flag? Thank you -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ 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] Qcache
Dear list, When processing the data for longitudinal analysis (or even for cross sectional) the -qcache has to be run before editing or after all the edits have been done? Thank you -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ 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.
Re: [Freesurfer] T1 error
Hello Bruce: My apologies for the incomplete way to raise the question. Anyway, we have solved it. Thank you very much. On Fri, Mar 17, 2017 at 3:30 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Manuel > > how do you know it is binary? Have you tried changing the window levels in > freeview when you view it? And in general when you report errors please > include the full screen output of what you ran, and in cases like this, and > image to illustrate the issue. > > cheers > Bruce > > > On Fri, 17 Mar 2017, Manuel Delgado wrote: > > After recon-all (recon-all -all -s 479_001), which finished without >> errors, >> the T1.mgz appears as a binary mask. I am using Freesurfer v 6.0 and >> Ubuntu >> 16.04. Please let me know if you need further files. >> Thank you, >> >> >> Manuel >> >> On Thu, Mar 16, 2017 at 4:09 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu> >> wrote: >> what is the error exactly? Please provide the recon-all.log file >> and a >> description of the problem >> >> >> On 03/16/2017 06:28 AM, Manuel Delgado wrote: >> > Dear list, >> > After recon-all the T1 seems to have an error. Has anybody had >> this >> > problem before? Please find attached the image. I guess I have >> to >> > recon-all again. I am using v 6.0 with Ubuntu 16.04. >> > Thank you. >> > >> > -- >> > *Manuel Delgado Alvarado, MD* >> > Neurology Department >> > Neuroimaging Unit >> > Valdecilla Biomedical Research Institute, IDIVAL >> > Santander, SPAIN >> > >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> 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. >> >> >> >> >> -- >> Manuel Delgado Alvarado, MD >> Neurology Department >> Neuroimaging Unit >> Valdecilla Biomedical Research Institute, IDIVAL >> Santander, SPAIN >> >> > ___________ > 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. > > -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ 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.
Re: [Freesurfer] T1 error
After recon-all (recon-all -all -s 479_001), which finished without errors, the T1.mgz appears as a binary mask. I am using Freesurfer v 6.0 and Ubuntu 16.04. Please let me know if you need further files. Thank you, Manuel On Thu, Mar 16, 2017 at 4:09 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > what is the error exactly? Please provide the recon-all.log file and a > description of the problem > > > On 03/16/2017 06:28 AM, Manuel Delgado wrote: > > Dear list, > > After recon-all the T1 seems to have an error. Has anybody had this > > problem before? Please find attached the image. I guess I have to > > recon-all again. I am using v 6.0 with Ubuntu 16.04. > > Thank you. > > > > -- > > *Manuel Delgado Alvarado, MD* > > Neurology Department > > Neuroimaging Unit > > Valdecilla Biomedical Research Institute, IDIVAL > > Santander, SPAIN > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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. > > -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ 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] T1 error
Dear list, After recon-all the T1 seems to have an error. Has anybody had this problem before? Please find attached the image. I guess I have to recon-all again. I am using v 6.0 with Ubuntu 16.04. Thank you. -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN ___ 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] (no subject)
Dear all, I am carefully starting up with the basics for analysis of 3T mri images. After having done the recon all I am about to begin the review and editting process where needed. However, I am now a bit overwhelmed. Is there any logical or recommended order to proceed with the several potential editting steps? Is it possible to edit all the parts (i.e. skull striping, wm, pial surface, etc) and performe an only final recon with all the needed flags? Best, Manuel ___ 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.
