[Freesurfer] White matter segmentation
Hi FreeSurfer I need the white matter segmentations, and I've looked at some e-mail correspondence and one answer I think I can use is the following: If you just want white matter, then better to create a mask from the aparc+aseg.mgz with mri_binarize with the --wm flag. doug I just don't understand what it means.. I do have the aparc+asset.mgz, but what is a mri_binarize and --wm flag? I don't have FreeSurfer installed on my on computer. All the best, Leise. ___ 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] modeling linear and quadratic effects simultaneously
That is an F-test that should more-or-less be an OR between your two t-tests. I don't know why you are seeing nothing, but the F-test can be non-intuitive. If you want to test an AND, then you will need to perform a conjunction (use mri_concat sig1.mgh sig2.mgh --conjunct --o conjunction.mgh doug On 10/02/2014 09:34 AM, Schweren, LJS (med) wrote: > > Dear Freesurfer experts, > > A while ago I sent the question below to the FS mailinglist, but it > was never answered… Would anyone be able to help me with this issue? > > Thank you very much in advance! > > Best wishes, > > Lizanne > > Dear Freesurfer experts, > > I am modelling multiple covariates (age, SES, nr of symptoms and nr of > > symptoms2) in one subject group. For the quadratic term I added a > column in > > the fsgd-file. I want to visualize the effect of nr of symptoms, either > > their linear or their quadratic effects. I therefore made two contrasts: > > The effect of symptoms: > > 0 0 1 0 > > And the effect of symptoms2: > > 0 0 0 1 > > I would like to model these two effects together in one contrast, to > visualize the total effect of symptoms. I tried the following contrast: > > 0 0 1 0 > > 0 0 0 1 > > But the result is very different from the two individual contrasts. I get > > large (non-overlapping) clusters of significant effect in the two separate > > contrasts, but with the combined contrasts I get none. > > What would be the appropriate contrast if I want > > to visualize all regions with the effects of symptoms, including both > linear AND quadratic effects? > > Thank you very much for your help > > Best wishes, Lizanne > > > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de > geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik > maken van dit bericht, het niet openbaar maken of op enige wijze > verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk > gesteld worden voor een incomplete aankomst of vertraging van dit > verzonden bericht. > > The contents of this message are confidential and only intended for > the eyes of the addressee(s). Others than the addressee(s) are not > allowed to use this message, to make it public or to distribute or > multiply this message in any way. The UMCG cannot be held responsible > for incomplete reception or delay of this transferred message. > > > ___ > 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.
Re: [Freesurfer] Reporting longitudinal change (pc1)
Hi Tudor, if you are trying to just construct a mean thickness map on a subset of your data (e.g. group 1, tp 1) then you could map and smooth the data using mris_preproc The easiest way to pass the subjects is to manually split your longitudinal qdec file into smaller ones to contain only the entries of group1 and tp1 etc and then pass this via the --qdec-long flag. Once the data is smoothed and mapped to fsaverage, you can use mri_concat to compute the mean of the stack (flag --mean). You can visualize it in tksurfer or freeview. Best, Martin On 10/02/2014 10:29 AM, Tudor Popescu wrote: Dear FS list (dear Martin), I have a 3 groups x 2 timepoints data set, and I did analyses in QDEC comparing my groups pairwise (2 at a time) in terms of the pre-to-post percentage change (pc1) in various surface-based metrics like thickness and area. Since a group contrast is a bit difficult for readers to interpret (it would read "where is the percentage change from pre to post greater for group 1 than for group 2?"), I am wondering what is, in fact, best to report, aside from showing images of the significant clusters. What commands would I have to use, exactly, to for instnace, compute the group means for pre and for post values for e.g. thickness, i.e. absolute values rather than differences? I think I only have the pc1's calculated, since if I select thickness (rather than thickness-pc1) in QDEC, it tells me it cannot find the smoothed files. Thanks! ___ Freesurfer mailing list 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 Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] represent and show the TRACULA outputs
Hi,what is the best way to represent and show the TRACULA outputs?I would use 3D rendering, reporting the ouput on structural image.I'm trying several option but the resolution and results are poorly satisfactory. Particularly, if I use free view and I upload the aparc+aseg+2mm.flt.nii or cortex as reference, I must modify the opacity to visualize the tract, but the quality is low. Is there a way to cut a window within the cortical redering to visualize the deep tract?Please, may you give me some suggestion?Thank you very much.Regards, Stefano ___ 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] problems with tracula pre-processing (bvecs)
Hi Michele - If there are large parts of the brain mask missing that overlap with one of the tracts, the reconstruction of that tract will keep failing. You should investigate why the aseg failed in that part of the brain. It's hard to guess without seeing the images. If there's a large artifact in the structural scan in that area then it may be irrecoverable, but if not it's worth fixing it. a.y On Wed, 1 Oct 2014, Michele Cavallari wrote: Hi Anastasia, thanks for your feedback. I checked both te aparc+aseg and the diffusion images. There is some underestimation of left insula and left temporal pole in the mask, corresponding to quite large missing (0 value) areas in the FA maps. I tried to re-run the -prep step using the "-prior" option and with no success: still getting a 'segmentation fault' error message (log and error files attached). Is there anything else I can try to analyze this case without having to re-run the segmentation/parcellation? And are there ways to improve the parcellation in those regions? Thanks On Wed, Sep 24, 2014 at 6:11 PM, Anastasia Yendiki wrote: Hi Michele - It seems like it's failing in the right uncinate again. From the error, I would guess that part of that tract is getting left out of the brain mask or something of that sort. Can you please check how that area looks in the aparc+aseg and in the diffusion data? a.y On Thu, 18 Sep 2014, Michele Cavallari wrote: Hi, I am having problems with tracula pre-processing for a case of a series I am analyzing. The processing worked without errors for two out of three cases I was running at the same time. I received a 'segmentation fault' error. I checked the FreeSurfer recon-all output, and it was completed without errors. I tried to re-process the case alone: got the very same outcome. I am enclosing the log file of the tracula processing of the case that's giving me an error. Let me know if you need more information/files. Thanks, -Michele On Tue, Sep 16, 2014 at 6:11 PM, Chris Watson wrote: I don't think that would change the results (significantly), so you would just be wasting processing time. It depends on the quality of your data. In this thread, as Anastasia said earlier, there is distortion around the L orbitofrontal cortex, which may have caused the problem Michele was having (reconstructing the L uncinate). But if you're *only* interested in a subset of the available tracts, you should probably comment out the others, if you want to save time. On 09/16/2014 07:18 AM, Barbara Kreilkamp wrote: Dear all, What does this mean? That tracula is more robust when running it seperately for the tracts I am interested in? Thanks, Barbara On Mon, Sep 15, 2014 at 4:44 PM, Michele Cavallari wrote: errata corrige: it did work! I had to re-run the whole thing including only that specific tract...and eventually it worked. On Fri, Sep 12, 2014 at 11:19 AM, Michele Cavallari wrote: Tried...unfortunately it didn't improve On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson wrote: You can try just re-running "trac-prep -prior" and "trac-paths" for the L uncinate and no other tracts On 09/11/2014 02:58 PM, Michele Cavallari wrote: So, I re-ran the case with the set reinit option. It "half" worked!...in the sense that the new results show the left uncinate right, but the right-side one is still a dot (see screenshot of the brain view from the bottom). Any further suggestion? Thanks. Inline image 2 On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari wrote: Thanks! it's running... On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp wrote: Hi Michele, Don't think there is anything wrong with the attached dmrirc.tutorial file. You definitely need to add the '-c' flag infront of the path to your configuration file. Right now it reads the path to your file as a flag, which is of course not what you want. Best, Barbara On 11/09/2014 17:49, Michele Cavallari wrote: Hi Anastasia, I am probably doing something wrong with the syntax of the dmrirc file. I get this error message trac-all -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial ERROR: flag /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial unrecognized -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial Could you please check the attached file? On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki wrote: Thanks, Michele.
[Freesurfer] Reporting longitudinal change (pc1)
Dear FS list (dear Martin), I have a 3 groups x 2 timepoints data set, and I did analyses in QDEC comparing my groups pairwise (2 at a time) in terms of the pre-to-post percentage change (pc1) in various surface-based metrics like thickness and area. Since a group contrast is a bit difficult for readers to interpret (it would read "where is the percentage change from pre to post greater for group 1 than for group 2?"), I am wondering what is, in fact, best to report, aside from showing images of the significant clusters. What commands would I have to use, exactly, to for instnace, compute the group means for pre and for post values for e.g. thickness, i.e. absolute values rather than differences? I think I only have the pc1's calculated, since if I select thickness (rather than thickness-pc1) in QDEC, it tells me it cannot find the smoothed files. Thanks! ___ 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] PhD position | Technische Universität München, Munich, Germany
PhD position in multiple sclerosis research Department of Neurology, Technische Universität München, Munich, Germany TUM-NIC, Neuroimaging Center, Munich, Germany The Department of Neurology of the Technische Universität München offers a PhD position in systems neuroscience research of Multiple Sclerosis. The project aims to investigate structural correlates of disability and biomarker patterns in patients with multiple sclerosis (MS) using MR imaging techniques. The candidate will investigate cortical pathology and lesion pathology in MS using state-of-the-art neuroimaging techniques. Applicants should have finished a university degree in medicine, psychology, biology, computer science or other relevant disciplines. Candidates should have strong analytical and organizational skills and prior experience with large cohort patient datasets is an advantage. Previous experience in analysis of structural/functional MR images (e.g., Freesurfer/FSL, SPM) is highly desired. Basic programming skills in for example Matlab or Unix shell scripting are a plus but not strictly required. Candidates who lack the aforementioned skills should have a strong motivation to develop these skills during their training. We are searching for candidates who are able to work independently and who have demonstrated excellent presentation and writing skills. The applicant will be expected to interact and collaborate with colleagues from different disciplines. Salary is according to the German TVöD. The position is available from January. The position is initially available for two years, the second year contingent on satisfactory progress. Extension beyond two years may be possible. Neuroimaging scanning facilities (MRI 3T scanner) and computer infrastructure are entirely available at the TUM Neuroimaging Center (TUM-NIC). Candidates may contact Prof Dr. Mark Mühlau (mueh...@lrz.tum.de) or Dr. Ruthger Righart (righ...@lrz.tum.de) for more detailed information. Applications including a letter of motivation and CV should be addressed to Prof. Dr. Mühlau by Email: mueh...@lrz.tum.de . ___ 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] modeling linear and quadratic effects simultaneously
Dear Freesurfer experts, A while ago I sent the question below to the FS mailinglist, but it was never answered... Would anyone be able to help me with this issue? Thank you very much in advance! Best wishes, Lizanne Dear Freesurfer experts, I am modelling multiple covariates (age, SES, nr of symptoms and nr of symptoms2) in one subject group. For the quadratic term I added a column in the fsgd-file. I want to visualize the effect of nr of symptoms, either their linear or their quadratic effects. I therefore made two contrasts: The effect of symptoms: 0 0 1 0 And the effect of symptoms2: 0 0 0 1 I would like to model these two effects together in one contrast, to visualize the total effect of symptoms. I tried the following contrast: 0 0 1 0 0 0 0 1 But the result is very different from the two individual contrasts. I get large (non-overlapping) clusters of significant effect in the two separate contrasts, but with the combined contrasts I get none. What would be the appropriate contrast if I want to visualize all regions with the effects of symptoms, including both linear AND quadratic effects? Thank you very much for your help Best wishes, Lizanne De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. ___ 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] Input files format
Ok, thanks a lot for your help! 2014-10-02 9:30 GMT-04:00 Bruce Fischl : > not other than the typical acquisition ones (T1-weighted, good contrast, > about 1mm voxel size, etc...) > > > On Thu, 2 Oct 2014, Svetlana Soloveva wrote: > > I guess it should be dicom, I need to ask our colleagues who acquire the >> data. Are there any other requirements for input images if they are dicom? >> Thanks a lot! >> >> 2014-10-02 9:18 GMT-04:00 Bruce Fischl : >> almost certainly yes. I assume they are dicom? >> On Thu, 2 Oct 2014, Svetlana Soloveva wrote: >> >> I see, thank you! In this case do you support the >> original MRIs if I can get >> them? It is my first time working with Freesurfer, >> so your input is very >> helpful. >> >> 2014-10-02 9:00 GMT-04:00 Bruce Fischl >> : >> I see. Sorry, I don't think we support it then >> >> Bruce >> On Thu, 2 Oct 2014, Svetlana Soloveva wrote: >> >> Hi Bruce, >> >> Thnaks! I think it is CTF MEG MRI file >> created by >> MRIConverter. >> >> 2014-10-02 8:35 GMT-04:00 Bruce Fischl >> : >> Hi Svetlana >> >> what format is *.mri? I don't >> think I've ever >> heard of it >> Bruce >> On Thu, 2 Oct 2014, Svetlana >> Soloveva wrote: >> >> Dear all, >> >> If I understand correctly, >> it is >> recommended to use >> original MRI files as an >> input. However, I have only >> *.mri file. >> First, I was >> able to run >> reconstruction following >> fieldtrip >> pipeline which >> includes some >> preprocessing of *.mri and >> writing >> resulting files >> in *.mgz format that can >> be used by Freesurfer. Is >> there any >> other way to >> work with *.mri files in >> Freesurfer without these >> preprocessing >> steps? >> >> Many thanks! >> >> Svetlana >> >> >> >> ___ >> 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] Input files format
not other than the typical acquisition ones (T1-weighted, good contrast, about 1mm voxel size, etc...) On Thu, 2 Oct 2014, Svetlana Soloveva wrote: I guess it should be dicom, I need to ask our colleagues who acquire the data. Are there any other requirements for input images if they are dicom? Thanks a lot! 2014-10-02 9:18 GMT-04:00 Bruce Fischl : almost certainly yes. I assume they are dicom? On Thu, 2 Oct 2014, Svetlana Soloveva wrote: I see, thank you! In this case do you support the original MRIs if I can get them? It is my first time working with Freesurfer, so your input is very helpful. 2014-10-02 9:00 GMT-04:00 Bruce Fischl : I see. Sorry, I don't think we support it then Bruce On Thu, 2 Oct 2014, Svetlana Soloveva wrote: Hi Bruce, Thnaks! I think it is CTF MEG MRI file created by MRIConverter. 2014-10-02 8:35 GMT-04:00 Bruce Fischl : Hi Svetlana what format is *.mri? I don't think I've ever heard of it Bruce On Thu, 2 Oct 2014, Svetlana Soloveva wrote: Dear all, If I understand correctly, it is recommended to use original MRI files as an input. However, I have only *.mri file. First, I was able to run reconstruction following fieldtrip pipeline which includes some preprocessing of *.mri and writing resulting files in *.mgz format that can be used by Freesurfer. Is there any other way to work with *.mri files in Freesurfer without these preprocessing steps? Many thanks! Svetlana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.p
Re: [Freesurfer] Input files format
I guess it should be dicom, I need to ask our colleagues who acquire the data. Are there any other requirements for input images if they are dicom? Thanks a lot! 2014-10-02 9:18 GMT-04:00 Bruce Fischl : > almost certainly yes. I assume they are dicom? > > On Thu, 2 Oct 2014, Svetlana Soloveva wrote: > > I see, thank you! In this case do you support the original MRIs if I can >> get >> them? It is my first time working with Freesurfer, so your input is very >> helpful. >> >> 2014-10-02 9:00 GMT-04:00 Bruce Fischl : >> I see. Sorry, I don't think we support it then >> >> Bruce >> On Thu, 2 Oct 2014, Svetlana Soloveva wrote: >> >> Hi Bruce, >> >> Thnaks! I think it is CTF MEG MRI file created by >> MRIConverter. >> >> 2014-10-02 8:35 GMT-04:00 Bruce Fischl >> : >> Hi Svetlana >> >> what format is *.mri? I don't think I've ever >> heard of it >> Bruce >> On Thu, 2 Oct 2014, Svetlana Soloveva wrote: >> >> Dear all, >> >> If I understand correctly, it is >> recommended to use >> original MRI files as an >> input. However, I have only *.mri file. >> First, I was >> able to run >> reconstruction following fieldtrip >> pipeline which >> includes some >> preprocessing of *.mri and writing >> resulting files >> in *.mgz format that can >> be used by Freesurfer. Is there any >> other way to >> work with *.mri files in >> Freesurfer without these preprocessing >> steps? >> >> Many thanks! >> >> Svetlana >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for >> the person to whom >> it is >> addressed. If you believe this e-mail was sent to >> you in error and the >> e-mail >> contains patient information, please contact the >> Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the >> e-mail was sent to you >> in error >> but does not contain patient information, please >> contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ 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] Input files format
almost certainly yes. I assume they are dicom? On Thu, 2 Oct 2014, Svetlana Soloveva wrote: I see, thank you! In this case do you support the original MRIs if I can get them? It is my first time working with Freesurfer, so your input is very helpful. 2014-10-02 9:00 GMT-04:00 Bruce Fischl : I see. Sorry, I don't think we support it then Bruce On Thu, 2 Oct 2014, Svetlana Soloveva wrote: Hi Bruce, Thnaks! I think it is CTF MEG MRI file created by MRIConverter. 2014-10-02 8:35 GMT-04:00 Bruce Fischl : Hi Svetlana what format is *.mri? I don't think I've ever heard of it Bruce On Thu, 2 Oct 2014, Svetlana Soloveva wrote: Dear all, If I understand correctly, it is recommended to use original MRI files as an input. However, I have only *.mri file. First, I was able to run reconstruction following fieldtrip pipeline which includes some preprocessing of *.mri and writing resulting files in *.mgz format that can be used by Freesurfer. Is there any other way to work with *.mri files in Freesurfer without these preprocessing steps? Many thanks! Svetlana ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Input files format
I see, thank you! In this case do you support the original MRIs if I can get them? It is my first time working with Freesurfer, so your input is very helpful. 2014-10-02 9:00 GMT-04:00 Bruce Fischl : > I see. Sorry, I don't think we support it then > > > Bruce > On Thu, 2 Oct 2014, Svetlana Soloveva wrote: > > Hi Bruce, >> >> Thnaks! I think it is CTF MEG MRI file created by MRIConverter. >> >> 2014-10-02 8:35 GMT-04:00 Bruce Fischl : >> Hi Svetlana >> >> what format is *.mri? I don't think I've ever heard of it >> Bruce >> On Thu, 2 Oct 2014, Svetlana Soloveva wrote: >> >> Dear all, >> >> If I understand correctly, it is recommended to use >> original MRI files as an >> input. However, I have only *.mri file. First, I was >> able to run >> reconstruction following fieldtrip pipeline which >> includes some >> preprocessing of *.mri and writing resulting files >> in *.mgz format that can >> be used by Freesurfer. Is there any other way to >> work with *.mri files in >> Freesurfer without these preprocessing steps? >> >> Many thanks! >> >> Svetlana >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Input files format
I see. Sorry, I don't think we support it then Bruce On Thu, 2 Oct 2014, Svetlana Soloveva wrote: Hi Bruce, Thnaks! I think it is CTF MEG MRI file created by MRIConverter. 2014-10-02 8:35 GMT-04:00 Bruce Fischl : Hi Svetlana what format is *.mri? I don't think I've ever heard of it Bruce On Thu, 2 Oct 2014, Svetlana Soloveva wrote: Dear all, If I understand correctly, it is recommended to use original MRI files as an input. However, I have only *.mri file. First, I was able to run reconstruction following fieldtrip pipeline which includes some preprocessing of *.mri and writing resulting files in *.mgz format that can be used by Freesurfer. Is there any other way to work with *.mri files in Freesurfer without these preprocessing steps? Many thanks! Svetlana ___ 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] Input files format
Hi Bruce, Thnaks! I think it is CTF MEG MRI file created by MRIConverter. 2014-10-02 8:35 GMT-04:00 Bruce Fischl : > Hi Svetlana > > what format is *.mri? I don't think I've ever heard of it > Bruce > > On Thu, 2 Oct 2014, Svetlana Soloveva wrote: > > Dear all, >> >> If I understand correctly, it is recommended to use original MRI files as >> an >> input. However, I have only *.mri file. First, I was able to run >> reconstruction following fieldtrip pipeline which includes some >> preprocessing of *.mri and writing resulting files in *.mgz format that >> can >> be used by Freesurfer. Is there any other way to work with *.mri files in >> Freesurfer without these preprocessing steps? >> >> Many thanks! >> >> Svetlana >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Displaying clusters from different QDEC analyses, overlapped
Dear FS list, I have significant clusters from several QDEC analyses (each one for a different DV< i.e. thickness, area, etc). I would like to generate a picture of a standard brain (talairach or MNI) with several of these clusters superimposed on the same brain, to show where there are e.g. regions of increased thickness and of decreased volume. I thought I could just load a standard brain in FreeView and then add the MGH files corresponding to all my contrasts of interest (after they've been MonteCarlo-corrected), in order to view all my clusters on the same brain. However, when I load any *mc-z.abs.th13.sig.cluster.mgh *in FreeView, the image seems to be blank, although in QDEC it shows a large blue cluster. I played around with the Min/Max/Level values in FreeView, but that didn't help. Can anyone suggest how to accomplish this? Thanks! Tudor ___ 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] Input files format
Hi Svetlana what format is *.mri? I don't think I've ever heard of it Bruce On Thu, 2 Oct 2014, Svetlana Soloveva wrote: Dear all, If I understand correctly, it is recommended to use original MRI files as an input. However, I have only *.mri file. First, I was able to run reconstruction following fieldtrip pipeline which includes some preprocessing of *.mri and writing resulting files in *.mgz format that can be used by Freesurfer. Is there any other way to work with *.mri files in Freesurfer without these preprocessing steps? Many thanks! Svetlana ___ 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.
