[Freesurfer] contrast matrix
Hi Freesurfer experts, When I perform the statistical analysis, I am very confused with the following questions: My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M), and two covariates. So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. 1) I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender and two covariates, but I don't know the rules for setting the contrasts for the interaction. The contrast matrix I used is: 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? If it is correct, how to explain the results, for example, what does the positive (or negative) clusters stand for? Or the clusters showed in the t-test statistical map are the regions that have the significant interaction? 2) When I perform the main effect of dignosis, is the following matrix I used correct? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 (I think it regressed out the effect of genotype and gender, that is it takes the genotype as a covariable) Or I should create another fsgd file, that has 4 classes: AF, AM, BF, BM. And I can use the matrix (0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0) to perform the main effect of diagnosis. which one is right? Any help will be very appreciated. Best wishes, Meng ___ 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] mri_surf2surf error
Hi Freesurfers, I'm trying to extracting thickness value for a ROI which is created by afni.I follow the workflows of Cortical Thickness of a Volume-defined ROI. The ROI mask and T1 volume file are all talairach transformed. When I map the thickness data to the fsaverage subject with mri_surf2surf,an error occured: dimension inconsistency in source data Number of surface vertices =154984 Number of value vertices =163842(23406*1*7) So I use reshape-factor 7 flag ,but it does not work, how can I fix this? Any advise would be appreciated! best Zhu ___ 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] mri_surf2surf error
Hi Zhu what is your command line? Bruce On Thu, 6 Sep 2012, zzy7...@mail.ustc.edu.cn wrote: Hi Freesurfers, I'm trying to extracting thickness value for a ROI which is created by afni.I follow the workflows of Cortical Thickness of a Volume-defined ROI. The ROI mask and T1 volume file are all talairach transformed. When I map the thickness data to the fsaverage subject with mri_surf2surf,an error occured: dimension inconsistency in source data Number of surface vertices =154984 Number of value vertices =163842(23406*1*7) So I use reshape-factor 7 flag ,but it does not work, how can I fix this? Any advise would be appreciated! best Zhu ___ 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] Frontiers Special Topic: Networks Underpinning Language Repetition
Sent on behalf of Marcelo L. Berthier and Matthew A. Lambon Ralph Dear colleagues As host editors of an innovative open access journal, Frontiers in Human Neuroscience, we are currently organizing a Special Topic centered around “Dissecting the function of networks underpinning language repetition”. We would be thrilled if you submitted an article to this Special Topic. A Frontiers’ Special Topic features the latest advances and challenges in hot research areas and attempts to unify the best researchers. It is a collection of at least ten articles, which may be comprised of any one of Frontiers’ article types. The proposed structure of this Special Topic is provided below and we would be happy to hear your suggestions. Hosting Journal: Frontiers in Human Neuroscience Topic Title: Dissecting the function of networks underpinning language repetition Host Editor(s): Marcelo L. Berthier, Matthew A. Lambon Ralph Topic description In the 19th century ground-breaking observations on aphasia by Broca and Wernicke suggested that language function depends on the activity of the cerebral cortex. At the same time, Wernicke and Lichtheim also elaborated the first large-scale network model of language which incorporated long-range and short-range (transcortical connections) white matter pathways in language processing. The arcuate fasciculus (dorsal stream) was traditionally viewed as the major language pathway for repetition, but scientists also envisioned that white matter tracts travelling through the insular cortex (ventral stream) and transcortical connections may take part in language processing. Modern cognitive neuroscience has provided tools, including neuroimaging, which allow the in vivo examination of short- and long-distance white matter pathways binding cortical areas essential for language. However, the state of the art on the neural correlates of language repetition reveals contradictory findings, with some researchers defending the role of the dorsal and ventral streams, whereas others argue that only cortical hubs (Sylvian parieto-temporal cortex [Spt]) are crucially relevant. An integrative approach would conceive that the interaction between these structures is essential for verbal repetition. For instance, different sectors of the cerebral cortex (e.g., Spt, inferior frontal gyrus/anterior insula) act as hubs dedicated to short-term storage of verbal information or articulatory planning and these areas in turn interact through forward and backward white matter projections. Importantly, white matter pathways should not be considered mere cable-like connections as changes in their microstructural properties correlate with focal cortical activity during language processing tasks. Despite considerable progress, many outstanding questions await response. Therefore, this topic welcomes contributors addressing the following questions (1) how white matter pathways instantiate dialogues between different cortical language areas; (2) what are the specific roles of different white matter pathways in language functions in normal and pathological conditions; (3) what are the language consequences of discrete damage to branches of the dorsal and ventral streams; 4) what are the consequences (e.g., release from inhibition) of damage to the left white matter pathways in contralateral ones and viceversa; (5) how these pathways are reorganised after brain injury; (5) can the involvement/sparing of white matter pathways be used in outcome prediction and treatment response; and (5) can the microstructure of white matter pathways be remodelled with intensive rehabilitation training or biological approaches. It is anticipated that the articles in this Research Topic will enhance the understanding of the neural organization of language repetition providing clues on therapeutic interventions of brain damaged individuals. Submission of original data is desirable, but we also encourage mini-reviews and perspective papers which offer provocative and insightful interpretations of the recent literature in the field. Abstract Submission Deadline: November 1, 2012 Researchers can participate by submitting a max. 1 page abstract/outline of work related to the focus of the research topic, through the Frontiers submission system, on or before the abstract submission deadline. Authors will be notified by the host editors whether their abstract has been accepted or rejected. Article Submission Deadline: May 1, 2013 You may find submit abstracts and find more information by clicking on this link: http://www.frontiersin.org/Human_Neuroscience/researchtopics/Dissecting_the_function_of_net/1078 We look forward to hearing from you Sincerely yours, Marcelo L. Berthier Matthew A. Lambon Ralph ___ 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
Re: [Freesurfer] mri_watershed and other errors.
OK. So do you have any other suggestions? Is there some minor difference between my version and yours that would explain this behavior. Other settings to try? Darren On Wed, Sep 5, 2012 at 4:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: our internal development version. On Wed, 5 Sep 2012, Darren Gitelman wrote: Bruce I used the following version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 Is that the same as the one you are using or are you referring to an internal development version? I will try Nick's suggestion as well. Darren On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I'm running it now with the current dev version and it's passed the skull stripping stage and it seems to have worked fine... On Wed, 5 Sep 2012, Nick Schmansky wrote: Darren, I forgot to mention that you'll need to add -clean-bm after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be retained and the new one will be saved as brainmask.auto.mgz. Nick On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote: Nick, List: Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s subjid -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s subjid -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s subjid -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s subjid -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren ___ 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. -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ 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] contrast matrix
On 09/06/2012 04:42 AM, Meng Li wrote: Hi Freesurfer experts, When I perform the statistical analysis, I am very confused with the following questions: My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M), and two covariates. So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. 1) I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender and two covariates, but I don't know the rules for setting the contrasts for the interaction. The contrast matrix I used is: 0.250.25 -0.25-0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? If it is correct, how to explain the results, for example, what does the positive (or negative) clusters stand for? Or the clusters showed in the t-test statistical map are the regions that have the significant interaction? This is correct. As with all interactions, the sign is hard to interpret. Most people will do post hoc analyses to help interpret the results. 2) When I perform the main effect of dignosis, is the following matrix I used correct? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 (I think it regressed out the effect of genotype and gender, that is it takes the genotype as a covariable) Or I should create another fsgd file, that has 4 classes: AF, AM, BF, BM. And I can use the matrix (0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0) to perform the main effect of diagnosis. which one is right? Your contrast is correct. doug Any help will be very appreciated. Best wishes, Meng ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Fw: Re: Re: mri_surf2surf error
Hi Bruce My command line is cd $SUBJECTS_DIR/subjid/surf mri_surf2surf \ --s con_52 \#It is my Processed freesurfer date --trgsubject fsaverage \ --hemi lh \ --sval lh.thickness \ --tval lh.thickness.fsaverage.mgh \ --reshape #or reshape-factor 7 Zhu -Original E-mail- From: Bruce Fischl fis...@nmr.mgh.harvard.edu Sent Time: 2012-9-6 20:15:35 To: zzy7...@mail.ustc.edu.cn Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2surf error Hi Zhu what is your command line? Bruce On Thu, 6 Sep 2012, zzy7...@mail.ustc.edu.cn wrote: Hi Freesurfers, I'm trying to extracting thickness value for a ROI which is created by afni.I follow the workflows of Cortical Thickness of a Volume-defined ROI. The ROI mask and T1 volume file are all talairach transformed. When I map the thickness data to the fsaverage subject with mri_surf2surf,an error occured: dimension inconsistency in source data Number of surface vertices =154984 Number of value vertices =163842(23406*1*7) So I use reshape-factor 7 flag ,but it does not work, how can I fix this? Any advise would be appreciated! best Zhu ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fw: Re: Re: mri_surf2surf error
can you send the full screen output as well? On Thu, 6 Sep 2012, zzy7...@mail.ustc.edu.cn wrote: Hi Bruce My command line is cd $SUBJECTS_DIR/subjid/surf mri_surf2surf \ --s con_52 \#It is my Processed freesurfer date --trgsubject fsaverage \ --hemi lh \ --sval lh.thickness \ --tval lh.thickness.fsaverage.mgh \ --reshape #or reshape-factor 7 Zhu -Original E-mail- From: Bruce Fischl fis...@nmr.mgh.harvard.edu Sent Time: 2012-9-6 20:15:35 To: zzy7...@mail.ustc.edu.cn Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2surf error Hi Zhu what is your command line? Bruce On Thu, 6 Sep 2012, zzy7...@mail.ustc.edu.cn wrote: Hi Freesurfers, I'm trying to extracting thickness value for a ROI which is created by afni.I follow the workflows of Cortical Thickness of a Volume-defined ROI. The ROI mask and T1 volume file are all talairach transformed. When I map the thickness data to the fsaverage subject with mri_surf2surf,an error occured: dimension inconsistency in source data Number of surface vertices =154984 Number of value vertices =163842(23406*1*7) So I use reshape-factor 7 flag ,but it does not work, how can I fix this? Any advise would be appreciated! best Zhu ___ 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 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
Re: [Freesurfer] Fw: Re: Re: mri_surf2surf error
Try using --srcsubject instead of --s. Also, remember to include the terminal output. Also, there's probably no need to reshape it. doug On 09/06/2012 10:54 AM, zzy7...@mail.ustc.edu.cn wrote: Hi Bruce My command line is cd $SUBJECTS_DIR/subjid/surf mri_surf2surf \ --s con_52 \#It is my Processed freesurfer date --trgsubject fsaverage \ --hemi lh \ --sval lh.thickness \ --tval lh.thickness.fsaverage.mgh \ --reshape #or reshape-factor 7 Zhu -Original E-mail- From: Bruce Fischlfis...@nmr.mgh.harvard.edu Sent Time: 2012-9-6 20:15:35 To: zzy7...@mail.ustc.edu.cn Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2surf error Hi Zhu what is your command line? Bruce On Thu, 6 Sep 2012, zzy7...@mail.ustc.edu.cn wrote: Hi Freesurfers, I'm trying to extracting thickness value for a ROI which is created by afni.I follow the workflows of Cortical Thickness of a Volume-defined ROI. The ROI mask and T1 volume file are all talairach transformed. When I map the thickness data to the fsaverage subject with mri_surf2surf,an error occured: dimension inconsistency in source data Number of surface vertices =154984 Number of value vertices =163842(23406*1*7) So I use reshape-factor 7 flag ,but it does not work, how can I fix this? Any advise would be appreciated! best Zhu ___ 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 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question about painting SPM results onto Freesurfer
Hi Doug, As Bruce suggested, you may give me some help. My question is: I paint SPM results onto Freesurfer surface, is it possible to get the size and name of clusters on the surface? Thanks Karry On Mon, Sep 3, 2012 at 10:16 PM, keepmoon keepmoon1...@googlemail.comwrote: Hi Bruce, Thanks for your answer! Yes. I would like to know the size of the cluster after painting on the surface. Expecting Doug's reply! Thanks in advance! Karry On Mon, Sep 3, 2012 at 7:51 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: you mean the size of the cluster on the surface? Yes, you can do that, but you'll need to wait for Doug's return for the details cheers Bruce On Mon, 3 Sep 2012, keepmoon wrote: Hi Bruce, Thanks for your detailed explaination! I have one more question about it! Is it possible to get cluster size for being painted SPM results on freesure surface (like getting the cluster size of cortical thickness in QDEC )? Is there any command getting it? Any idea will be appreciated! Thanks! Karry On Mon, Sep 3, 2012 at 5:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Karry painting is done by mri_vol2surf and you can use it to specify how you want the sampling to be done. We typically sample the volume halfway our from the gray/white boundary, or sometimes a bit lower to avoid vascular artifacts at the pial surface. That said, it is quite flexible and you can use it to sample however you wish (e.g. average over the bottom third of cortex, etc). When we sample we don't inspect the value, just grab it from the volume and assign it to the surface so if there are significant cluster that aren't intersected by the sampling band you specify they will not appear on the surface. cheers Bruce On Sun, 2 Sep 2012, keepmoon wrote: Hello everyone, I just read the information about paintig SPM results onto Freesurfer (http://surfer.nmr.mgh.**harvard.edu/fswiki/SpmPaintinghttp://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting **). It shows how to painting SPM results from statistic step (ex. spmT.img) to surface space. I tested the procedure and it worked. But I don't understand what is displayed on Freesurfer surface. Are all the significant differences from SPM statistic results are displayed on this surface? or some part of t values are displayed (which part)? As cortical thickness displayed on surface, each thickness value is painted on each vertex. But here t-value image from SPM is volume image, how to paint it on surface? Someone could give a little detailed explaination?? Thanks in advance Karry 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/**compliancelinehttp://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] creating a gca file from .mgz files
The command line to get the aseg was: Mri_convert -rt nearest -c file containing all valued label masks.nii.gz aseg.mgz Fslmaths was used to match label values to the colour lut and combine them all into one file. Thanks, Jeff On 2012-09-05, at 1:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what is your mri_convert command line? On Wed, 5 Sep 2012, Jeff Thompson wrote: Hello, I got mri_ca_train to complete and to produce a .gca file, which looks to be what is expected after splitting it up into means/labels/priors files. The problem was the norm.mgz file. I ended up copying and renaming the T1.mgz file to replace the norm.mgz file, and it seemed to work in mri_ca_train. I am now having trouble with the aseg.mgz file in mri_normalize. It states that the aseg.mgz file needs to be conformed. When I conform the image the label values are way off. I tried the mri_convert conform with the rt nearest , but the label values seemed to still be off. The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90. Any recommendations to solve this problem? Thank you, Jeff Thompson Subject: Re: [Freesurfer] creating a gca file from .mgz files From: ni...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Wed, 29 Aug 2012 19:56:09 -0400 i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration. for mri_convert, be sure to include the flag -rt nearest which overrides the default resample type of 'interpolate', which is not appropriate for labeled volumes. n. On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote: Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz with mri_convert without throwing all of the label values off. This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an error stating ERROR: mri_ca_train check found 1 subjects with bad labels! Thanks, Jeff Thompson __ CC: freesurfer@nmr.mgh.harvard.edu From: fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthomp...@hotmail.com Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train
Re: [Freesurfer] creating a gca file from .mgz files
and when you say it is way off what do you mean? Is the intensity volume conformed in the same way? On Thu, 6 Sep 2012, Jeff Thompson wrote: The command line to get the aseg was: Mri_convert -rt nearest -c file containing all valued label masks.nii.gz aseg.mgz Fslmaths was used to match label values to the colour lut and combine them all into one file. Thanks, Jeff On 2012-09-05, at 1:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what is your mri_convert command line? On Wed, 5 Sep 2012, Jeff Thompson wrote: Hello, I got mri_ca_train to complete and to produce a .gca file, which looks to be what is expected after splitting it up into means/labels/priors files. The problem was the norm.mgz file. I ended up copying and renaming the T1.mgz file to replace the norm.mgz file, and it seemed to work in mri_ca_train. I am now having trouble with the aseg.mgz file in mri_normalize. It states that the aseg.mgz file needs to be conformed. When I conform the image the label values are way off. I tried the mri_convert conform with the rt nearest , but the label values seemed to still be off. The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90. Any recommendations to solve this problem? Thank you, Jeff Thompson Subject: Re: [Freesurfer] creating a gca file from .mgz files From: ni...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Wed, 29 Aug 2012 19:56:09 -0400 i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration. for mri_convert, be sure to include the flag -rt nearest which overrides the default resample type of 'interpolate', which is not appropriate for labeled volumes. n. On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote: Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz with mri_convert without throwing all of the label values off. This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an error stating ERROR: mri_ca_train check found 1 subjects with bad labels! Thanks, Jeff Thompson __ CC: freesurfer@nmr.mgh.harvard.edu From: fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthomp...@hotmail.com Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training on
Re: [Freesurfer] surface area of a patch in fsaverage_sym white and pial surface
Yes, it is probably best to do it with those as those have the averages across the subjects used to create the atlas. If you just use the area of the cluster on the pial, it will be somewhat smaller. doug On 09/06/2012 01:53 PM, Ritobrato Datta wrote: Hi Doug, I need to dump the surface area of a patch in fsaverage_sym lh. But I need to dump the value for fsaverage_sym pial surface, white surface and inflated surface. I noticed that in the folder freesurfer/subjects/fsaverage_sym/surf/ there is ?h.white.avg.area.mgh ?h.pial.avg.area.mgh What are these ? Can I just apply my patch/mask/label on ?h.white.avg.area.mgh and ?h.pial.avg.area.mgh to get the corresponding scalars ? Please let me know. We are finishing up this paper and need these values as soon as possible. Any help will be very much appreciated. Thanks a lot Rito -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
