Re: [Freesurfer] TRACULA analyses in glmfit
Hi Anastasia, Thanks for the clarification. I am happy to hear that you are working on that! As the byvoxel data includes MNI coordinates, I though it could be possible to assemble them to MNI 3D space. Thanks again! Pedro Rosa. On Monday, July 6, 2015 at 12:19 PM, Anastasia Yendiki wrote: > > Hi Pedro - The point-wise stats from tracula are a 1D sequence of values, > so they cannot be analyzed with functions that work on 2D data on the > surface or 3D data in the volume. At present, you'd have to do a seperate > analysis for every point along the tract. It's on my list to implement a > more comprehensive and principled solution for this and will hopefully get > around to it soon! > > BTW, the diffusion measures are extracted by tracula in the native space, > not in a template space. An average path in template space is produced in > case you want to visualize something on an average brain, but all the > pointwise and average FA/MD/etc values are extracted in the native DWI > space of each subject. > > Best, > a.y > > On Sun, 5 Jul 2015, Pedro Rosa - GMail wrote: > > > Dear Developers, > > Tracula’s Statistics wiki suggests one to use the statistical software of > > choice. > > Could it be glmfit? > > For that, I think I would need to concatenate each tract-by-voxel diffusion > > data > > from each subject (e.g., each diffusion data of course separately) in > > common space > > (e.g., MNI) and then input it to mri_glmfit / mri_glmfit-sim, whose output > > sig.mgh > > would be loaded in Freeview as a heatmap. > > I understood that diffusion data in Tracula is saved in .txt files, which > > cannot be > > inputed into mri_preproc or mri_label2vol. Is it possible to use glmfit > > with Tracula > > outputs? > > Thanks in advance, > > Pedro Rosa. > > > > > ___ > 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 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] TRACULA analyses in glmfit
Dear Developers, Tracula’s Statistics wiki suggests one to use the statistical software of choice. Could it be glmfit? For that, I think I would need to concatenate each tract-by-voxel diffusion data from each subject (e.g., each diffusion data of course separately) in common space (e.g., MNI) and then input it to mri_glmfit / mri_glmfit-sim, whose output sig.mgh would be loaded in Freeview as a heatmap. I understood that diffusion data in Tracula is saved in .txt files, which cannot be inputed into mri_preproc or mri_label2vol. Is it possible to use glmfit with Tracula outputs? Thanks in advance, Pedro Rosa. ___ 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] dt_recon
Thanks, Doug! Pedro Rosa On Monday, May 11, 2015 at 6:51 PM, Douglas N Greve wrote: > It sounds like you did the right thing. > > On 05/10/2015 02:41 PM, Pedro Rosa - GMail wrote: > > Dear developers, > > I am running an analysis with dt_recon, and it seems that my DWI files > > are organized into three series (one larger, and two smaller, that I > > believe are ADC and Trace). Inputing a DICOM file to dt_recon > > generates a .nii file from one of the series only (the larger one, > > once it has many more .dcm files). Thus, it ignores the smaller series. > > This is the first time I am working with DWI series, so I not quite > > sure if this way of organizing data is usual. > > I would appreciate help in regard of how to deal with this data and > > input it into dt_recon. > > Regards, > > Pedro Rosa. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto: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 (mailto: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 > (http://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 (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 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] dt_recon
Dear developers, I am running an analysis with dt_recon, and it seems that my DWI files are organized into three series (one larger, and two smaller, that I believe are ADC and Trace). Inputing a DICOM file to dt_recon generates a .nii file from one of the series only (the larger one, once it has many more .dcm files). Thus, it ignores the smaller series. This is the first time I am working with DWI series, so I not quite sure if this way of organizing data is usual. I would appreciate help in regard of how to deal with this data and input it into dt_recon. Regards, Pedro Rosa. ___ 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] Amazon EC2 for FreeSurfer 5.3
Thanks, Pedro! Pedro Rosa On Wednesday, April 29, 2015 at 7:11 PM, Pedro Paulo de Magalhães Oliveira Junior wrote: > Yes. CerebralVol.com (http://CerebralVol.com) does it > > - > Pedro Paulo de Magalhães Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br (http://www.netfilter.com.br) > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > On Wed, Apr 15, 2015 at 9:47 PM, Pedro Rosa - GMail (mailto:pedrogomesr...@gmail.com)> wrote: > > Dear FreeSurfer users, > > Has anyone succeeded in running FreeSurfer 5.3 in a cloud processing > > system, such as Amazon EC2? > > I have seen prior posts in regard of FreeSurfer 5.1 > > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021181.html), > > but not for 5.3. > > Regards, > > Pedro Rosa. > > ___ > > 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 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] Amazon EC2 for FreeSurfer 5.3
Dear FreeSurfer users, Has anyone succeeded in running FreeSurfer 5.3 in a cloud processing system, such as Amazon EC2? I have seen prior posts in regard of FreeSurfer 5.1 (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021181.html), but not for 5.3. Regards, Pedro Rosa. ___ 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] Insula
Hi, Thanks a lot, Bruce. These are from a 1.5T GE Signa scanner, with a T1-SPGR sequence with 0.86x0.86x1.5mm voxel size, echo time 5.2ms, resolution time 21.7ms, flip angle 20. This is an older sample we have, and I intent to replicate earlier SPM analyses but now using FreeSurfer. I acknowledge the low contrast problem, but I am having success in correcting topological errors in the temporal lobe, and only these insula problems show to be harder to deal with. Your help will be very appreciated! I am now putting the file (PedroRosa.zip) Best,, Pedro Rosa On Tuesday, April 7, 2015 at 9:29 AM, Bruce Fischl wrote: > sure, upload it and we will take a look. Can you tell us a bit about the > acquisition? It's hard to tell for sure with the parcellation overlaid, > but it looks *very* low contrast, which I'm sure is making things harder > > cheers > Bruce > On Mon, 6 Apr 2015, Pedro Rosa - Gmail > wrote: > > > Dear FreeSurfers, > > I was correcting the topology of some subjects, and could not fix some > > subjects whose insula is misplaced into the temporal lobe / subcortical > > regions. Inspecting wm.mgz in tkmedit, it seems that there are wm voxels > > into the hippocampus, perhaps leading surfaces to be built there. Removing > > them, however, did not help (actually, it seems that it made things worse). > > Can you help me? I can upload the subject if it you think it is suitable. > > Many thanks in advance, > > Pedro Rosa. > > > > ___ > 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 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] Insula
Dear FreeSurfers, I was correcting the topology of some subjects, and could not fix some subjects whose insula is misplaced into the temporal lobe / subcortical regions. Inspecting wm.mgz in tkmedit, it seems that there are wm voxels into the hippocampus, perhaps leading surfaces to be built there. Removing them, however, did not help (actually, it seems that it made things worse). Can you help me? I can upload the subject if it you think it is suitable. Many thanks in advance, Pedro Rosa. ___ 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 - varying geometries
Thanks, Martin. It is unfortunate to hear such news, but they are of course accurate. Hopefully this affects a small subset of subjects, and I will be able to add a covariate to it. Regards, Pedro Rosa. On Wednesday, April 1, 2015 at 12:30 PM, Martin Reuter wrote: > Hi Pedro, > > there is really no way to fix it. Especially if all you subjects changed > acquisition. If it is only a small subset, you can then include a co-variable > to account for this in your stats. You should then also test whether one > group has more of these cases than the other, or if it is distributed evenly > (in case you run a group analysis). If you are interested in analyzing other > co-variates (drug dose) you need to test if there is a correlation with > acquisition, etc. > > Reslicing will not help at all. Adding another reslicing step to only some > images will clearly bias results. > > If this change in acquisition has happened for most or all your subjects, you > can scan a subset back-to-back (with removal from scanner), with the > different protocols to see how large the effect is. The problem here is that > you need to scan a decent number to trust those results. > > Best, Martin > > > On 04/01/2015 11:21 AM, Pedro Rosa wrote: > > Hi Martin, > > Thank you for your answer. > > Is there a way to fix it? Can reslicing help? > > Or to try compenate for it in the processing or statistics? > > Regards > > > > -- > > Pedro Rosa > > > > > > On Apr 1, 2015, at 12:13, Martin Reuter > (mailto:mreu...@nmr.mgh.harvard.edu)> wrote: > > > > > Hi Pedro, > > > > > > yes, there was a bug (well, not really a bug but the check was > > > oversensitive). It was testing too many image parameters, some of them > > > could be problematic (e.g. different voxel sizes across time), and some > > > not. > > > > > > Looking at your attached files, you can see that the voxel sizes differ > > > significantly between the baseline and the follow-up > > > Baseline: > > > dimensions: 256 x 256 x 124 > > >voxel sizes: 0.8594, 0.8594, 1.5000 > > > Follow-up: > > > dimensions: 256 x 256 x 124 > > >voxel sizes: 1.0938, 1.0938, 1.5000 > > > > > > This can induce a bias. You need to keep imaging parameters fixed in a > > > longitudinal study, else you'll not know if changes are anatomical > > > changes or induced by the different imaging. > > > > > > Best, Martin > > > > > > On 04/01/2015 06:43 AM, Pedro Rosa - Gmail wrote: > > > > Dear FreeSurfers, I have read in the Mailing list > > > > (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32753.html > > > > and others) other users asking questioning in regard of a Warning from > > > > FreeSurfer 5.3 longitudinal pipeline (-base step): > > > > \n*** > > > > WARNING: Image geometries differ across time, maybe due to aquisition > > > > changes? This can potentially bias a longitudinal study! Will continue > > > > in 10s. > > > > ***\n > > > > I am working in a sample with a longotudinal design which receives > > > > this warn, although there was no change in hardware, and (supposedly) > > > > the acquisition protocol was the same. As requested by Martin in former > > > > posts in the Mailing List, I attached the output from mri_info > > > > */rawavg.mgz. I would like to know if these differences should be > > > > considered a bias in a longitudinal study and, if they should, if there > > > > is a way to fix it. Regards, Pedro Rosa. > > > > > > > > > > > > > > > > ___ Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School > > > Assistant in Neuroscience Dept. of Radiology, Massachusetts General > > > Hospital Dept. of Neurology, Massachusetts General Hospital Research > > > Affiliate Computer Science and Artificial Intelligence Lab, Dept. of > > > Electrical Engineering and Computer Science, Massachusetts Institute of > > > Technology A.A.Martinos Center for Biomedi
[Freesurfer] Longitudinal - varying geometries
Dear FreeSurfers, I have read in the Mailing list (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32753.html and others) other users asking questioning in regard of a Warning from FreeSurfer 5.3 longitudinal pipeline (-base step): \n*** WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ***\n I am working in a sample with a longotudinal design which receives this warn, although there was no change in hardware, and (supposedly) the acquisition protocol was the same. As requested by Martin in former posts in the Mailing List, I attached the output from mri_info */rawavg.mgz. I would like to know if these differences should be considered a bias in a longitudinal study and, if they should, if there is a way to fix it. Regards, Pedro Rosa. baseline Description: Binary data fup Description: Binary data ___ 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] Cortical Misegmentation
Hi, Bruce. I am currently putting the file (Well-C0-T1w-023-20050425_124.zip) - it will take a while. I was able to make it a lot better using the Topological Defect correction in tkmedit. Is it suitable for this task? I have not tried adding control points. This is an older data with a quite long follow-up, so unfortunately I can not change the acquisition. Sorry, I am unaware of the type of receive coil that was used. Thanks, Pedro Rosa. On Friday, March 6, 2015 at 10:28 AM, Bruce Fischl wrote: > Hi Pedro > > the instructions are at: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > have you tried control points in the temporal wm? And what receive coil did > you use? You might be better off with something like 1.1mm isotropic if you > can change the acquisition > > cheers > Bruce > > On Fri, 6 Mar 2015, > Pedro Rosa wrote: > > > Sure. How can I do it? > > > > Sent from my iPhone > > > > On Mar 6, 2015, at 00:01, Bruce Fischl > (mailto:fis...@nmr.mgh.harvard.edu)> > > wrote: > > > > Can you put it on our ftp site instead? > > > > > > > > On Mar 5, 2015, at 9:37 PM, Pedro Rosa > (mailto:pedrogomesr...@gmail.com)> > > wrote: > > > > Hi, > > It will upload in an hour, Iguess: > > https://www.dropbox.com/sh/n9talmyxiafdt56/AADFttKFv3erLqDd48OpjQsna > > ?dl=0 > > Thanks a lot, > > Pedro. > > > > On Mar 5, 2015, at 23:32, Bruce Fischl > > mailto:fis...@nmr.mgh.harvard.edu)> wrote: > > > > Hmmm, if you upload it we will take a look > > Bruce > > > > > > > > On Mar 5, 2015, at 9:26 PM, Pedro Rosa - Gmail > > mailto:pedrogomesr...@gmail.com)> wrote: > > > > That’s from a 1.5T-SPGR GE scanner with > > 0.86x0.86x1.5mm voxel size, echo time 5.2ms, > > repetition time 21.7ms, angle 20, FOV 22, > > matrix size 256x192mm. > > > > Pedro Rosa > > > > On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl > > wrote: > > > > What are your acquisition parameters, > > voxel size etc...? > > > > > > > > On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail > > mailto:pedrogomesr...@gmail.com)> wrote: > > > > Hi, Bruce. > > Yes, it it the T1.mgz. Is it a large > > topological error? Can I correct it > > editing wm.mgz? > > Thanks, > > Pedro. > > > > On Thursday, March 5, 2015 at 10:52 PM, > > Bruce Fischl wrote: > > > > What is the background > > image? Is it the t1 that > > your reconned? Can you give > > us the details about it? > > > > > > > > On Mar 5, 2015, at 8:28 PM, Pedro > > Rosa - Gmail > > mailto:pedrogomesr...@gmail.com)> wrote: > > > > Dear FreeSurfer, > > I have found several > > subjects to have temporal > > lobe misegmentations > > (usually neocortical, as > > attached, but sometimes > > mesial tempporal), and less > > frequently in the insula. > > I could find in the manual > > editing page from the Wiki a > > way to fix this. How should > > I do it? > > Thanks a lot, > > Pedro Rosa. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > > 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 > > > > ___ > > Freesu
Re: [Freesurfer] Cortical Misegmentation
That’s from a 1.5T-SPGR GE scanner with 0.86x0.86x1.5mm voxel size, echo time 5.2ms, repetition time 21.7ms, angle 20, FOV 22, matrix size 256x192mm. Pedro Rosa On Thursday, March 5, 2015 at 11:11 PM, Bruce Fischl wrote: > What are your acquisition parameters, voxel size etc...? > > > > On Mar 5, 2015, at 9:08 PM, Pedro Rosa - Gmail (mailto:pedrogomesr...@gmail.com)> wrote: > > > Hi, Bruce. > > Yes, it it the T1.mgz. Is it a large topological error? Can I correct it > > editing wm.mgz? > > Thanks, > > Pedro. > > > > On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote: > > > > > What is the background image? Is it the t1 that your reconned? Can you > > > give us the details about it? > > > > > > > > > > > > On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail > > (mailto:pedrogomesr...@gmail.com)> wrote: > > > > > > > Dear FreeSurfer, > > > > I have found several subjects to have temporal lobe misegmentations > > > > (usually neocortical, as attached, but sometimes mesial tempporal), and > > > > less frequently in the insula. > > > > I could find in the manual editing page from the Wiki a way to fix > > > > this. How should I do it? > > > > Thanks a lot, > > > > Pedro Rosa. > > > > > > > > > > > > ___ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > > > 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 > ___ > 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 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] Cortical Misegmentation
Hi, Bruce. Yes, it it the T1.mgz. Is it a large topological error? Can I correct it editing wm.mgz? Thanks, Pedro. On Thursday, March 5, 2015 at 10:52 PM, Bruce Fischl wrote: > What is the background image? Is it the t1 that your reconned? Can you give > us the details about it? > > > > On Mar 5, 2015, at 8:28 PM, Pedro Rosa - Gmail (mailto:pedrogomesr...@gmail.com)> wrote: > > > Dear FreeSurfer, > > I have found several subjects to have temporal lobe misegmentations > > (usually neocortical, as attached, but sometimes mesial tempporal), and > > less frequently in the insula. > > I could find in the manual editing page from the Wiki a way to fix this. > > How should I do it? > > Thanks a lot, > > Pedro Rosa. > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ > 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 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] Cortical Misegmentation
Dear FreeSurfer, I have found several subjects to have temporal lobe misegmentations (usually neocortical, as attached, but sometimes mesial tempporal), and less frequently in the insula. I could find in the manual editing page from the Wiki a way to fix this. How should I do it? Thanks a lot, Pedro Rosa. ___ 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] RAM Replace
Dear all, I would like to know whether a RAM memory replacement in a Mac computer would change FreeSurfer 5.3 processing. I have a sample that was almost completely processed, but there are a few subjects whose acquisition are yet to be done. I would like know whether I could process such images after the RAM replacement without biasing the study. The change would be from a Markvision without ECC (error-correction code) to a Kingston with ECC. Thanks in advance, Pedro Rosa. ___ 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] Thin Surface
Thanks, Bruce. I pasted the mri_segment and mris_make_surfaces I found in three subjects’ logs. Expert opts would be -seg-wlo and -seg-ghi? Which values would be reasonable? Do they depend on scanning characteristics or do you have a sort of standard parameters for the software? Regards, Pedro Rosa. Subject 1: #@# WM Segmentation Mon Feb 16 09:08:56 BRST 2015 \n mri_segment brain.mgz wm.seg.mgz \n doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 105.0 +- 4.5 [80.0 --> 125.0] GM (72.0) : 70.1 +- 13.5 [30.0 --> 96.0] setting bottom of white matter range to 83.6 setting top of gray matter range to 97.1 Subject 2: WM (105.0): 105.6 +- 4.6 [80.0 --> 125.0] GM (70.0) : 68.4 +- 13.5 [30.0 --> 96.0] setting bottom of white matter range to 81.9 setting top of gray matter range to 95.4 Subject 3: WM (105.0): 105.6 +- 4.3 [80.0 --> 125.0] GM (71.0) : 69.2 +- 13.9 [30.0 --> 96.0] setting bottom of white matter range to 83.2 setting top of gray matter range to 97.1 —— Subject 1: \n mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs Subject2 lh \n only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/filled.mgz... reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/brain.finalsurfs.mgz... reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/wm.mgz... 14199 bright wm thresholded. 1723 bright non-wm voxels segmented. reading original surface position from /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/surf/lh.orig... computing class statistics... border white:347738 voxels (2.07%) border gray 336007 voxels (2.00%) WM (95.0): 96.2 +- 6.5 [70.0 --> 110.0] GM (85.0) : 81.4 +- 13.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.8 (was 70) setting MAX_BORDER_WHITE to 105.5 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 44.5 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 31.3 (was 40) Subject 2: setting MIN_GRAY_AT_WHITE_BORDER to 70.2 (was 70) setting MAX_BORDER_WHITE to 106.6 (was 105) setting MIN_BORDER_WHITE to 84.0 (was 85) setting MAX_CSF to 56.4 (was 40) setting MAX_GRAY to 93.4 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 77.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 42.5 (was 40) Subject 3: WM (97.0): 97.9 +- 6.2 [70.0 --> 110.0] GM (87.0) : 83.8 +- 13.5 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 107.2 (was 105) setting MIN_BORDER_WHITE to 85.0 (was 85) setting MAX_CSF to 57.9 (was 40) setting MAX_GRAY to 94.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 78.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.4 (was 40) On Wednesday, February 18, 2015 at 7:58 PM, Bruce Fischl wrote: > can you check mri_segmet and mris_make_surfaces and see if the > auto-detected intensity parameters are reasonable? Things like max gray > at csf border and such. If not, you can set them explicitly using the > expert opts - this usually works > Bruce > On Wed, 18 Feb 2015, Pedro Rosa - Gmail > wrote: > > > Hi, > > I am resending it once I could not find it in the archives. > > Thanks, > > Pedro. > > > > Dear Freesurfers, > > I am working on a 1.5T MPRAGE sample of first-episode psychosis and > > controls, and have found that some subjects end up having thin cortical > > surfaces with frequent unsegmented deep sulci. I think this was worse with > > FreeSurfer 5.3 than with FreeSurfer 5.1. I attached some screen shots of > > aparc+aseg labeling T1.mgz from a few of these subjects. > > This seems to be a widespread cortical issue, although it was heterogeneous > > across subjects (some of them seemed to have the “caudal half" of both > > hemispheres adequately segmented), and trying to simply rerun those > > subjects was not very helpful. Should I manually work on them, rerun > > recon-all with distinct parameters, or just discard them? > > Regards, > > Pedro Rosa. > > > > > ___ > 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 pati
[Freesurfer] LME Contrasts - Longitudinal Analysis
Dear Freesurfer List, Reading the Wiki for the GLM procedures, I understood that that covariates that are “0” in the contrast matrix are “regressed out” (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V). I would like to know if this is also true for the LME contrasts (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels), and if this applies both for categorical (e.g., gender) and continuous variables (e.g., age in years). Thank you very much in advance, Pedro Rosa. ___ 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.
