Re: [Freesurfer] Longitudinal processing
I see now. If the orientation information is incorrect, this will continue to be a problem. It sounds like you have access to the dicoms? If so, it's better to wait and use those. Allison On Mon, 8 Jul 2013, Jonathan Holt wrote: Allison I'm running the following recon-all -all -s -i path/to/nifti attatched is the error recon log I've already gone over this with bruce, martin. It seems as if the 001.mgz, orig.mgz, and orig_nu.mgz all have incorrect orientations. This is coming straight out of the nifti files I've passed and these mgz's are generated before the recon-all process exits with errors. On Jul 8, 2013, at 1:37 PM, Allison Stevens Player wrote: In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running? On Mon, 8 Jul 2013, Jonathan Holt wrote: As I'm having trouble importing nifti files into the first step of the longitudinal work flow, I'm wondering if I can use volumes generated from recon-all -s for the second and third steps of the workflow. jon ___ 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___ 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] Longitudinal processing
In short, the answer is yes. The 2nd and 3rd steps will take the subject ID and find the relevant files. But I would expect the first step to take nifti just fine. Can you send the command you are running? On Mon, 8 Jul 2013, Jonathan Holt wrote: > As I'm having trouble importing nifti files into the first step of the > longitudinal work flow, I'm wondering if I can use volumes generated from > recon-all -s for the second and third steps of the workflow. > > jon > ___ > 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 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] question about autorecon2-cp, autorecon-pial and autorecon-wm flags
That's correct. On Thu, 14 Mar 2013, Mehul Sampat wrote: Hi Folks,I was looking at the autorecon2-cp, autorecon-pial and autorecon-wm flags in recon-all help and also here http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags My interpretation is when I use autorecon-pial, I only need the command: recon-all --autorecon-pial -s subject While for autorecon2-cp and autorecon2-wm we need the command: recon-all -autorecon2-cp -autorecon3 -s subject recon-all -autorecon2-wm -autorecon3 -s subject since for autorecon2-cp and autorecon2-wm only a subset of stages are processed as described in recon-all help: -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 Thanks Mehul ___ 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 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] Estimate of number of manual edits and time to complete in 100subject sample
Hi Kev, For the two scenarios you mentioned, here are my best estimates. I assume a healthy, adult population scanned with our recommended sequences. Any other type of dataset (pediatric, one with some type of pathology, one acquired long ago using a less than optimal sequence or coil, etc.) would likely differ by a lot in terms of time estimates. 1. fMRI on good quality 3T Maybe 25 out of 100 need some kind of intervention, including restarting a process that may have failed along the way. I would expect these 25 to have something terribly wrong with them to make them unacceptable for fMRI analysis but something that is most likely easily fixed by an automatic intervention. I'd estimate a half hour for each of the 25 or an hour for each to be extremely conservative. 2. Cortical thickness on good quality 3T Maybe 50-75 out of 100 need some kind of intervention, depending on which areas you might focus on if you're not only interested in global thickness. Edits on half of those will be very small, 15-30 minutes a case. Edits on the other half may be more time consuming, 30 minutes to 1 hour. Allison On Tue, 5 Mar 2013, Schumman Resonance wrote: This is a question for the FS community in general, I gather there is variability around this, but rather than an exact number and time, I was hoping for an estimate on how many scans would I expect to require manual edits(any of the check points recommended in the tutorials) as well as an estimate of the time it takes to go through them. For the sake of the argument, take a sample of 100 subjects. Thanks, Kev ___ 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 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] "cannot allocate memory" issue
There are instructions on how to check it here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach On Mon, 14 May 2012, Borzello, Mia wrote: > Hey Allison, > > Thanks for you help. What do you mean by check your talairach? I'll hold off > on using a different set of dicoms, and make that my last resort since it > takes a day to complete. > Thanks, > m > ________ > From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] > Sent: Monday, May 14, 2012 3:16 PM > To: Borzello, Mia > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] "cannot allocate memory" issue > > Hi Mia, > You may want to check your talairach to make sure that looks okay. If > that's not causing the problem, you can edit the wm.mgz to remove the > cerebellum and then rerun and this should fix the problem. > Allison > > On Mon, 14 May 2012, Borzello, Mia wrote: > >> It says that it couldn't open rh.orig.nofix and lh.orig.nofix. On the popup >> image, it doesn't look like the skull is present, but it does look like the >> cerebellum is. >> >> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] >> Sent: Monday, May 14, 2012 1:28 PM >> To: Borzello, Mia >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] "cannot allocate memory" issue >> >> You can do: >> tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix >> >> When you downloaded FreeSurfer, you would have also received the subject >> "bert" who is a good example to compare to. He will likely be located in: >> $FREESURFER_HOME/subjects/bert >> >> If you do the same command above for bert: >> tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix >> >> You'll see what the filled.mgz should look like. >> Allison >> >> On Mon, 14 May 2012, Borzello, Mia wrote: >> >>> How do I check this? (Apologies for my ignorance.) So I might need to just >>> use a different set of dicoms then? >>> >>> thanks, >>> Mia >>> >>> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] >>> Sent: Monday, May 14, 2012 1:02 PM >>> To: Borzello, Mia >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] "cannot allocate memory" issue >>> >>> It looks like there is too huge a topology error for it to continue: >>> >>> CORRECTING DEFECT 23 (vertices=143258, convex hull=19937) >>> Excessive topologic defect encountered: could not allocate -729782272 >>> edges for retessellation >>> Cannot allocate memory >>> >>> I would suggested looking at the filled.mgz to make sure skull and/or >>> cerebellum are not included. >>> Allison >>> >>> On Mon, 14 May 2012, Borzello, Mia wrote: >>> >>>> Hi all, >>>> >>>> I was wondering if you could help me figure out why the recon isn't >>>> running to completion. I've attached the log file (recon-all.log), but >>>> it's unclear to me what I should do to fix this problem. I tried to >>>> compute the lh.pial, but I guess it was never made in the recon. >>>> >>>> Thanks so much, >>>> Mia >>>> >>> >>> >>> >> >> >> > > > ___ 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] "cannot allocate memory" issue
Hi Mia, You may want to check your talairach to make sure that looks okay. If that's not causing the problem, you can edit the wm.mgz to remove the cerebellum and then rerun and this should fix the problem. Allison On Mon, 14 May 2012, Borzello, Mia wrote: > It says that it couldn't open rh.orig.nofix and lh.orig.nofix. On the popup > image, it doesn't look like the skull is present, but it does look like the > cerebellum is. > ____________ > From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] > Sent: Monday, May 14, 2012 1:28 PM > To: Borzello, Mia > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] "cannot allocate memory" issue > > You can do: > tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix > > When you downloaded FreeSurfer, you would have also received the subject > "bert" who is a good example to compare to. He will likely be located in: > $FREESURFER_HOME/subjects/bert > > If you do the same command above for bert: > tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix > > You'll see what the filled.mgz should look like. > Allison > > On Mon, 14 May 2012, Borzello, Mia wrote: > >> How do I check this? (Apologies for my ignorance.) So I might need to just >> use a different set of dicoms then? >> >> thanks, >> Mia >> >> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] >> Sent: Monday, May 14, 2012 1:02 PM >> To: Borzello, Mia >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] "cannot allocate memory" issue >> >> It looks like there is too huge a topology error for it to continue: >> >> CORRECTING DEFECT 23 (vertices=143258, convex hull=19937) >> Excessive topologic defect encountered: could not allocate -729782272 >> edges for retessellation >> Cannot allocate memory >> >> I would suggested looking at the filled.mgz to make sure skull and/or >> cerebellum are not included. >> Allison >> >> On Mon, 14 May 2012, Borzello, Mia wrote: >> >>> Hi all, >>> >>> I was wondering if you could help me figure out why the recon isn't running >>> to completion. I've attached the log file (recon-all.log), but it's unclear >>> to me what I should do to fix this problem. I tried to compute the lh.pial, >>> but I guess it was never made in the recon. >>> >>> Thanks so much, >>> Mia >>> >> >> >> > > > ___ 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] "cannot allocate memory" issue
If you happen to have another MPRAGE for this subject, sure, you can try it. Allison On Mon, 14 May 2012, Borzello, Mia wrote: > would it be worth it at this point, to use another set of dicoms? > thanks, > m > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia > Sent: Monday, May 14, 2012 1:37 PM > To: Allison Stevens Player > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] "cannot allocate memory" issue > > It says that it couldn't open rh.orig.nofix and lh.orig.nofix. On the popup > image, it doesn't look like the skull is present, but it does look like the > cerebellum is. > ____ > From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] > Sent: Monday, May 14, 2012 1:28 PM > To: Borzello, Mia > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] "cannot allocate memory" issue > > You can do: > tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix > > When you downloaded FreeSurfer, you would have also received the subject > "bert" who is a good example to compare to. He will likely be located in: > $FREESURFER_HOME/subjects/bert > > If you do the same command above for bert: > tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix > > You'll see what the filled.mgz should look like. > Allison > > On Mon, 14 May 2012, Borzello, Mia wrote: > >> How do I check this? (Apologies for my ignorance.) So I might need to just >> use a different set of dicoms then? >> >> thanks, >> Mia >> >> From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] >> Sent: Monday, May 14, 2012 1:02 PM >> To: Borzello, Mia >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] "cannot allocate memory" issue >> >> It looks like there is too huge a topology error for it to continue: >> >> CORRECTING DEFECT 23 (vertices=143258, convex hull=19937) >> Excessive topologic defect encountered: could not allocate -729782272 >> edges for retessellation >> Cannot allocate memory >> >> I would suggested looking at the filled.mgz to make sure skull and/or >> cerebellum are not included. >> Allison >> >> On Mon, 14 May 2012, Borzello, Mia wrote: >> >>> Hi all, >>> >>> I was wondering if you could help me figure out why the recon isn't running >>> to completion. I've attached the log file (recon-all.log), but it's unclear >>> to me what I should do to fix this problem. I tried to compute the lh.pial, >>> but I guess it was never made in the recon. >>> >>> Thanks so much, >>> Mia >>> >> >> >> > > ___ > 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 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] "cannot allocate memory" issue
You can do: tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix When you downloaded FreeSurfer, you would have also received the subject "bert" who is a good example to compare to. He will likely be located in: $FREESURFER_HOME/subjects/bert If you do the same command above for bert: tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix You'll see what the filled.mgz should look like. Allison On Mon, 14 May 2012, Borzello, Mia wrote: > How do I check this? (Apologies for my ignorance.) So I might need to just > use a different set of dicoms then? > > thanks, > Mia > ____________ > From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] > Sent: Monday, May 14, 2012 1:02 PM > To: Borzello, Mia > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] "cannot allocate memory" issue > > It looks like there is too huge a topology error for it to continue: > > CORRECTING DEFECT 23 (vertices=143258, convex hull=19937) > Excessive topologic defect encountered: could not allocate -729782272 > edges for retessellation > Cannot allocate memory > > I would suggested looking at the filled.mgz to make sure skull and/or > cerebellum are not included. > Allison > > On Mon, 14 May 2012, Borzello, Mia wrote: > >> Hi all, >> >> I was wondering if you could help me figure out why the recon isn't running >> to completion. I've attached the log file (recon-all.log), but it's unclear >> to me what I should do to fix this problem. I tried to compute the lh.pial, >> but I guess it was never made in the recon. >> >> Thanks so much, >> Mia >> > > > ___ 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] longitudinal analysis 5.0 or 5.1?
Hi Cat, You'll need to rerun those subjects with 5.1 to be able to use the longitudinal analysis in 5.1. You can also find a detailed explanation on how to go about edits here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits Allison On Wed, 18 Apr 2012, Cat Chong wrote: Dear Freesurfers: We have a large group of subjects (for which we have two time-points) that were run through the recon-all stream using 5.0. We have done no manual editing yet. We would like to do a longitudinal analysis of these subjects using 5.1 by comparing both time-points for each subject. Is that a possibility using 5.1? Also, at what point should I correct for topographical defects, or make edits to the white matter or brain mask volume? Should I edit both time-points separately first and then initiate the longitudinal analysis? If so, could I do the manual editing using 5.1? thank you very much for your help, cheers, cat ___ 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 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] Segmentation
Hi Jordan, I'm not sure I understand your question. If you run -make all, it will run recon-all again starting at the earliest step in which there are files that were changed that affect that step. It will run all the way through to the end as each step affects the next one. This will change your stats which are produced in autorecon3. Allison On Apr 16, 2012, at 10:28 AM, Jordan Pierce wrote: > Hi, > > We're trying to edit the aseg segmentation and reconstruct it. If we run > 'recon-all -s subject -make all' does that depend on any information from the > surfaces or brainmask volume, or are the stats independent of that? > > Thank you, > > Jordan Pierce > Graduate Student > Behavioral and Brain Sciences Program > Psychology Department > The University of Georgia > ___ > 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 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] created a new subcortical atlas; what's next?
Anthony, Depending on what version of FreeSurfer you are running, you would have to run the command it would normally run to create the aseg but substitute in your atlas. For example, in v5.1: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1 You can see the step next to -calabel: mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz Allison On Fri, 13 Apr 2012, Anthony Dick wrote: Hello, I successfully created a new subcortical atlas for the cerebellum (at least I think I did--not sure how to check it without running a new segmentation). If I want to apply this to many brains, I think I want to run: recon-all -subcortseg -subjid How do I tell it to call, e.g., RB_all_withskull_2012-04-13.gca instead of e.g., RB_all_withskull_2008-03-26.gca. Basically, I want to apply the new cerebellar parcellation to existing freesurfed brains. Anthony ___ 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 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] freeview
You can make a copy of the LUT and remove all regions from it you don't want to see. Then when you load you volume, specify you want to use this new LUT and you will only see the ROIs in it. Allison On Apr 12, 2012, at 11:40 PM, Adil Javed wrote: > Hi, > is there any way to overlay only certain regions of interest from the LUT > table and not all of them in freeview or tkmedit over a T1 image? I want to > just display certain areas or ROIs. > > thanks, > AJ > ___ > 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 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] correcting pial surface
Julia, could you send a snapshot of the area in question? On Apr 2, 2012, at 5:33 AM, "Richter, Julia" wrote: > Dear freesurfer experts, > > I have several subjects whose cortical grey matter isn't included in the pial > surface. Is there any possibility to correct the pial surface? I added > control points to the white matter to bring the regional white matter > intensity up, but it didn't change anything in the grey matter. > > Thanks for your help, Julia > > ___ > 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 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] Running FS on deskulled dataset
Hi Darshan, There are instructions on how to do this here: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F Allison On Tue, 27 Mar 2012, Darshan P wrote: I have an MRI volume dataset, which is deskulled beforehand . Is it possible to run recon-all with an option stating to not deskull the data. Regards Darshan ___ 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 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] Spot Opened in Boston FreeSurfer course
Hi everyone, We had a last minute drop-out from our Boston FreeSurfer course which takes place April 2nd through the 4th. If anyone is interested in taking this spot, please let me know. Details about the course content, the registration fee, and other logistics can be found here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Allison ___ 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] FreeSurfer Course in Amsterdam!
Hi everyone, The Department of Radiology at VU University Medical Center in Amsterdam, Netherlands is hosting a FreeSurfer Course on June 27th through June 29th. Registration is now open. You can find details about course as well as the registration form on the following website: http://www.freesurfercourseamsterdam.nl/ Questions about the Amsterdam course should go to Veronica Popescu (i...@freesurfercourseamsterdam.nl). Hope to see you there, Allison ___ 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] Question regarding control points
Although the white surface finds its place based on intensity, it's starting point is the wm.mgz. So if there are no voxels in the wm.mgz in the area you mention, drawing in some voxels combined with the intensity changes that come from the control points may help. Allison On Mar 12, 2012, at 6:53 PM, Martijn Steenwijk wrote: > @ Louis, no I didn't correct the WM mask yet. But since it's a step clearly > 'behind' correcting the skull strip and adding control points, and it takes a > lot of work to accurately draw the WM mask, I would prefer to automate things > as much as possible... > > @Alan, thanks for your suggestion - although 1 CP for 2 voxels appears to be > a lot. Tomorrow I'll check whether adding CP's helps. > > On Mon, Mar 12, 2012 at 3:47 PM, Alan Francis > wrote: > Hi Martijn: > > In our lab, we basically add a greater density of control points - almost 1 > CP for every 2 voxels. This way the corrected pial looks closer to what's > expected. > > best, > > Alan > > BIDMC > > On Mon, Mar 12, 2012 at 5:38 AM, Martijn Steenwijk > wrote: > Dear all, > > I've been correcting a recon with controlpoints and correction of the skull > strip. Although the result is a lot better, still a part of the temporal lobe > is missed, although I have been putting control points in this area. Is there > a way to improve this? See attached image (left: pre-correction, right: > post-correction). > > Best, > Martijn > > ___ > 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 ___ 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] Recommended reconstruction wiki
Okay, I'll look into it and fix the wiki page if needed. However, -make all should do the same for you. Allison On Mar 2, 2012, at 8:23 AM, Martijn Steenwijk wrote: > Hi Allison, > > But when I run -autorecon-cp it complains that the option does not exist. I'm > using FS5.1.. > > msteenwj@lnx-rad-03 freesurfer51 % recon-all -subjid P102_corr -autorecon-cp > ERROR: Flag -autorecon-cp unrecognized. > -subjid P102_corr -autorecon-cp > Linux lnx-rad-03 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 > x86_64 x86_64 GNU/Linux > > recon-all -s P102_corr exited with ERRORS at Fri Mar 2 14:23:15 CET 2012 > > For more details, see the log file > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > Best, > Martijn > > On Fri, Mar 2, 2012 at 2:15 PM, Allison Stevens Player > wrote: > Hi Martijn, > autorecon-cp is correct, we start the process a bit earlier now. But even > better, regardless of what edits you make, you can rerun with "recon-all > -make all" and it will start at the earliest needed step. (Although running > from autorecon2 after the skullstrip fix is correct as well). > Allison > > On Mar 2, 2012, at 6:11 AM, Martijn Steenwijk > wrote: > >> Dear all, >> >> On http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction it is >> indicated that -autorecon-cp should be added if control points are added. >> Shouldn't this be -autorecon2-cp? >> >> Furthermore, suppose control points are added and -autorecon2-cp has been >> runned. If I then correct the skull strip (as indicated in the wiki) and >> want to rerun, do I have to call -autorecon2-cp then, or can I just run >> -autorecon2 -autorecon3? >> >> Best, >> Martijn >> ___ >> 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.
Re: [Freesurfer] Recommended reconstruction wiki
Hi Martijn, autorecon-cp is correct, we start the process a bit earlier now. But even better, regardless of what edits you make, you can rerun with "recon-all -make all" and it will start at the earliest needed step. (Although running from autorecon2 after the skullstrip fix is correct as well). Allison On Mar 2, 2012, at 6:11 AM, Martijn Steenwijk wrote: > Dear all, > > On http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction it is > indicated that -autorecon-cp should be added if control points are added. > Shouldn't this be -autorecon2-cp? > > Furthermore, suppose control points are added and -autorecon2-cp has been > runned. If I then correct the skull strip (as indicated in the wiki) and want > to rerun, do I have to call -autorecon2-cp then, or can I just run > -autorecon2 -autorecon3? > > Best, > Martijn > ___ > 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 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] How to only do spatial normalization in FreeSurfer.
I'm sorry, I misunderstood. This website may be more helpful: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration On Feb 24, 2012, at 10:39 AM, Long wrote: > Thank you Allison, however, I checked the website and it is said that > FreeSurfer transform the orig volume to the MNI305 atlas, so the spatial > normalization in FreeSurfer is still done in volume space but not in surface > space, right? > > Best, > Xiangyu > > On Fri, Feb 24, 2012 at 5:20 AM, Allison Stevens Player > wrote: > Maybe you can apply the transform using mri_convert or mri_vol2vol created > during autorecon1. Is that what you are looking for? > > http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable > > > On Feb 22, 2012, at 11:26 AM, Long wrote: > > > Dear all, > > > > I had EPI images and T1 image and the EPI images are already co-registered > > to T1 image in their native space. I also run 'recon' on T1 image. I'd like > > to try surface-based spatial normalization in FreeSurfer, so how can I only > > do the spatial normalization of EPI images in FreeSurfer, i.e., transform > > EPI images from native space to mni152 space, then I could have > > surface-based normalized EPI images. > > > > Best, > > Xiangyu > > ___ > > 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.
Re: [Freesurfer] How to only do spatial normalization in FreeSurfer.
Maybe you can apply the transform using mri_convert or mri_vol2vol created during autorecon1. Is that what you are looking for? http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable On Feb 22, 2012, at 11:26 AM, Long wrote: > Dear all, > > I had EPI images and T1 image and the EPI images are already co-registered to > T1 image in their native space. I also run 'recon' on T1 image. I'd like to > try surface-based spatial normalization in FreeSurfer, so how can I only do > the spatial normalization of EPI images in FreeSurfer, i.e., transform EPI > images from native space to mni152 space, then I could have surface-based > normalized EPI images. > > Best, > Xiangyu > ___ > 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 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] white matter edits
Vincent, Some may look like holes but as you mention are just sulci being cut through by that plane. A way to check if it is the above is to put the cursor on the surface that creates this hole and then toggle to the other views (sagittal, axial, coronal). It will become clearer whether it is a sulcus or not in the other views based on where the cursor is located. It takes some getting used to in order to differentiate the errors that appear as holes vs. sulci if you are not used to looking at the anatomy this way. But the sulci will be in the same areas brain to brain and you will get used to ignoring them. You can also use tksurfer to help identify true errors (they will look like holes or bumps on the surface). Allison On Feb 22, 2012, at 6:12 PM, cloud.c...@me.com wrote: > According to the tutorial at > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits, we > should be looking for these holes in the white surface, but when I looked at > my processed data using tkmedit SUBJECT brainmask.mgz -aux wm.mgz -surfs, I > saw many such holes. They seem to be ubiquitous throughout all 20 of the > brains I have processed. Some might be true mistakes in the white matter > surface, but I thought maybe some might just be holes that appear because of > the shape of sulci moving through 3D space.Or perhaps my Talairach is > off? Is there any material that instructs how to tell the difference between > holes which need to be fixed and those that don't? > > Thank you, > Vincent > ___ > 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 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] Fixing talairach registration
I don't think there is any other way. Is the talairach really that bad in all of your data? It won't recon without fixing it? On Feb 22, 2012, at 6:17 PM, cloud.c...@me.com wrote: > After reading the tutorial at > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach, I understand > that I should be using > "tkregister2 --mgz --s SUBJECT --fstal --surf orig" when editing my talairach > transform. I have been somewhat successful at this, but I was wondering if > there might be another way to adjust talairach registration, perhaps by > specifying anterior/posterior commissure alignment, etc? > ___ > 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 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.
