Re: [Freesurfer] reg-feat2anat failure
This file is created when you run reg-feat2anat and should be the one that gets changed with --manxfm func2anat. You can handle this differently if you 1. Manually edit the anat2exf.register.dat so that it is relatively close (no need to be perfect) cd feat/reg/freesurfer tkregister2 --mov ../../example_func.nii.gz --reg anat2exf.register.dat --surfs 2. Run bbregister: cp anat2exf.register.dat backup.anat2exf.register.dat # Make a backup bbregister --mov ../../example_func.nii.gz --init-reg anat2exf.register.dat --reg anat2exf.register.dat --bold this second step will fine-tune your hand-edited version. Then go back and run aparc2feat, etc. doug Michelle Umali wrote: Hi Doug, The file that changed was exf2std.register.dat. How do I specify that I wanted that anat2exf.register.dat is supposed to be edited? At what point in the processing stream does this occur? Did editing exf2std.register.dat do anything? Thanks. Michelle On Tue, Oct 18, 2011 at 2:17 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The registration that should be used for all of these is anat2exf.register.dat found in feat/reg/freesurfer. Can you verify that that was the one that you manually changed? Look at the time stamp as compared to the other files in that folder. doug Michelle Umali wrote: Hi Doug, I am using reg-feat2anat on the feat directory of each run. reg-feat2anat --feat feadir.feat --subject XX Then I checked and adjusted the registration with: reg-feat2anat --feat featdir.feat --manual Next I checked and adjusted the registration to the standard with: reg-feat2anat --feat featdir.feat --manxfm func2std To generate cortical binary masks I used: aparc2feat --feat featdir.feat --annot BA fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10 -uthr 10 featdir.feat/reg/freesurfer/V1_l.nii.gz To generate subcortical binary masks I did: aseg2feat --feat featdir.feat --aseg aparc+aseg fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz -thr 54 -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz When I looked at the masks in FSLview and checked the masks against the other atlases, everything was off even after painstakingly editing the registrations. Is there something I am doing wrong? Thanks. Michelle On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: How are you generating the masks? doug Michelle Umali wrote: Hi Freesurfers, I've run reg-feat2anat on several subjects in order to generate binary masks to use in an FSL ppi. For 3 subjects, this completely failed. When I looked at the fsl's own registration of fsl feat 2 standard (via tkregister2), the registration is fine, but after running reg-feat2anat, the registration of the feat to the freesurfer anatomical and the feat to standard are completely off. I manually fixed and saved the registration edits via reg-feat2anat --manual, but when I generated the masks again, they were totally wrong still. When looking at freesurfer's feat to standard registration, it looks like all the brains weren't tall enough in the saggital view. Am I supposed to stretch the feat brain to fit? How can I fix this so that the masks are accurate? Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[Freesurfer] problem with generating cesvar.nii
Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] problem with generating cesvar.nii
Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. What you are trying to get is the expected variance of your difference between the ces files (as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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.
Re: [Freesurfer] trac-all results
Hi Ping - Do the corresponding brain masks in diffusion space (dlabel/diff/aparc+aseg_mask.bbr.nii.gz and aparc+aseg_mask.flt.nii.gz) now cover the entire brain well, after the aparc+aseg fixes? a.y On Tue, 18 Oct 2011, Ping-Hong Yeh wrote: Hi Anastasia, I got fixed of the aparc+aseg (see aparc+aseg.png) in one of problematic data and re-ran the trac-all following your suggestions. However, the segmented forceps major using FLIRT still not getting good result (see flt.png) though BBR one is OK (see bbr.png). Similarly the segmented L CST using BBR looks weird, but the ones using FLIRT seem OK. It appear the problems are not simply due to the poor segmentation from the T1 recon-all. Any further suggestions? BR, Ping On Fri, Oct 14, 2011 at 11:04 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping-Hong, Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask will be extracted from the DWI data by the bet tool, instead of using the aparc+aseg. But, and this is a big but, TRACULA uses the aparc+aseg to constrain the tractography solutions, i.e. the aparc+aseg is where the UnderLying Anatomy in TRACULA comes from. So the quality of the trac-all results depend on the quality of the aparc+aseg regardless of where your mask came from. a.y On Fri, 14 Oct 2011, Ping-Hong Yeh wrote: Hi Anastasia, Can trac-all just use the mask in diffusion native space (by setting usemaskanat = 0? ) so I get around the T1 segmentation problem from FS recon? It seems that there is no quick answer on fixing the aparc+aseg? Thank you, p On Tue, Oct 11, 2011 at 10:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I'll have to refer you back to the freesurfer list for that one. There are people with much more expertise than me on troubleshooting the recon-all stream. Once you get your recons fixed, you'll have to rerun all trac-all steps except 1.1 (image corrections). On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: The original aparc+aseg are not good, at least for these two cases. So which parameters in recon-all should be tweaked? On Tue, Oct 11, 2011 at 5:38 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Is the original aparc+aseg from the freesurfer recon not good either (from mri/aparc+aseg.mgz)? Or is it messed up only after registration into diffusion space (dlabel/diff/aparc+aseg.flt.nii.gz, dlabel/diff/aparc+aseg.bbr.nii.gz)? This will determine if the freesurfer recon needs to be fixed or if the registration needs to fixed. On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: yeap, the aparc+aseg_masks are not good. Any way to fix this? Thanks. On Tue, Oct 11, 2011 at 5:00 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I see, the mask may be the answer to the initialization failures! It seems like the fmajor you sent me also has its endings masked out? That'd cause it to fail. I wish I'd thought of this earlier! With usemaskanat = 1, the mask that's used is a slightly dilated version of the aparc+aseg from the FS recon, mapped to diffusion space. So if the aparc+aseg has those parts missing, or if the diffusion-anatomical registration is not good, parts will be masked out that shouldn't. The anatomical mask can be found in dlabel/diff/aparc+aseg_mask* (if you've run both flirt and bbregister registrations, there'll be 2 of them). Does this mask look like something went wrong? On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: I used the default, i.e. set usemaskanat =1, but it looks that tracts were not reconstructed at the place where it was masked out (see the cross-bar at L_unc.png). I still have no luck in fixing the initialization issue (see fmajor.png for example). Thanks. On Tue, Oct 11, 2011 at 3:19 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - If you're using the anatomical brain as a mask (set usemaskanat = 1, which is the default), then the diffusion-based mask won't have an effect on your outputs. BTW, have you had any luck with your initialization issues? Sorry I haven't had another chance to look at your data since we last emailed, I got bogged down with some other stuff. a.y On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: Hi Anastasia, I'd like to lower the bet threshold value by set thrbet = 0.01 for skull-stripping because some of the brains have been cut, but it does not seem to make any changes (see attached). Any suggestion? Thank you, Ping On Fri, Sep 30, 2011 at 12:09 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Yes! Please add the set reinit = 1 to the file that you pass with -c. On Fri, 30 Sep 2011, Ping-Hong Yeh wrote: so I should pass with the -c argument instead? On Fri, Sep 30, 2011 at 12:04 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: That file gets overwritten by whatever is in the file that you pass with the -c argument to trac-all. Sorry for the confusion. On Fri, 30 Sep 2011, Ping-Hong Yeh wrote: I edited the file under scripts/dmrirc.local
Re: [Freesurfer] problem with generating cesvar.nii
Thanks Doug. Just one related question. Should I also generate a new ffxdof.dat file for this map? I assumed that ffxdof depends on the number of subjects (session) and since number of subjects (sessions) is the same between the two groups then I can use those values, generated by isxconcat-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. What you are trying to get is the expected variance of your difference between the ces files (as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] problem with generating cesvar.nii
It should be roughly the sum of the dofs of the individual subjects. Why are you using a fixed-effects model? doug SHAHIN NASR wrote: Thanks Doug. Just one related question. Should I also generate a new ffxdof.dat file for this map? I assumed that ffxdof depends on the number of subjects (session) and since number of subjects (sessions) is the same between the two groups then I can use those values, generated by isxconcat-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. What you are trying to get is the expected variance of your difference between the ces files (as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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] problem with generating cesvar.nii
Do you suggest using random-effect model? Is there any problem with using a fix-effect model (other than the fact that by using this model we can not predict response of subjects outside our population)? On Wed, Oct 19, 2011 at 3:07 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: It should be roughly the sum of the dofs of the individual subjects. Why are you using a fixed-effects model? doug SHAHIN NASR wrote: Thanks Doug. Just one related question. Should I also generate a new ffxdof.dat file for this map? I assumed that ffxdof depends on the number of subjects (session) and since number of subjects (sessions) is the same between the two groups then I can use those values, generated by isxconcat-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. What you are trying to get is the expected variance of your difference between the ces files (as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.niimap1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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
Re: [Freesurfer] problem with generating cesvar.nii
If you don't care about extending your results beyond your sample, then an FFx is fine. doug SHAHIN NASR wrote: Do you suggest using random-effect model? Is there any problem with using a fix-effect model (other than the fact that by using this model we can not predict response of subjects outside our population)? On Wed, Oct 19, 2011 at 3:07 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It should be roughly the sum of the dofs of the individual subjects. Why are you using a fixed-effects model? doug SHAHIN NASR wrote: Thanks Doug. Just one related question. Should I also generate a new ffxdof.dat file for this map? I assumed that ffxdof depends on the number of subjects (session) and since number of subjects (sessions) is the same between the two groups then I can use those values, generated by isxconcat-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. What you are trying to get is the expected variance of your difference between the ces files (as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group-average of the same subjects (generated by using separate isxconcat-sess commands ), and now I want to see the difference map. To do so, I used mris_calc as below. mris_calc -o diff_map/rh.ces.nii map1/rh.ces.nii sub map2/rh.ces.nii Also, to generate the rh.cesvar.nii file I used this command: mris_calc -o diff_map1/rh.cesvar.nii map1/rh.cesvar.nii sub map2/rh.cesvar.nii But then when I used the glmfit with WLS option as below: mri_glmfit --y rh.ces.nii --osgm --glmdir rh.ffx.osgm.wls --nii --mask ../rh.mask.nii --yffxvar rh.cesvar.nii --ffxdofdat ../ffxdof.dat --surf fsaverage rh --wls rh.cesvar.nii I faced an error saying: Error: MRInormWeights: values less than or eq to 0 which I assumed is related to an error in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 tel:617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] trac-all results
The mask sort of covers the whole brain (see attached). It may be due to the display thresholding, when I viewed the path.pd.nii.gz using fslview, the tract actually has been recovered as compared to the previous one (old_path.png). However, the path.pd still does seem normal, i.e. with quite a few extraordinary high intensity (probability, yellow)? Thanks. ping On Wed, Oct 19, 2011 at 2:52 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Do the corresponding brain masks in diffusion space (dlabel/diff/aparc+aseg_mask.bbr.nii.gz and aparc+aseg_mask.flt.nii.gz) now cover the entire brain well, after the aparc+aseg fixes? a.y On Tue, 18 Oct 2011, Ping-Hong Yeh wrote: Hi Anastasia, I got fixed of the aparc+aseg (see aparc+aseg.png) in one of problematic data and re-ran the trac-all following your suggestions. However, the segmented forceps major using FLIRT still not getting good result (see flt.png) though BBR one is OK (see bbr.png). Similarly the segmented L CST using BBR looks weird, but the ones using FLIRT seem OK. It appear the problems are not simply due to the poor segmentation from the T1 recon-all. Any further suggestions? BR, Ping On Fri, Oct 14, 2011 at 11:04 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping-Hong, Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask will be extracted from the DWI data by the bet tool, instead of using the aparc+aseg. But, and this is a big but, TRACULA uses the aparc+aseg to constrain the tractography solutions, i.e. the aparc+aseg is where the UnderLying Anatomy in TRACULA comes from. So the quality of the trac-all results depend on the quality of the aparc+aseg regardless of where your mask came from. a.y On Fri, 14 Oct 2011, Ping-Hong Yeh wrote: Hi Anastasia, Can trac-all just use the mask in diffusion native space (by setting usemaskanat = 0? ) so I get around the T1 segmentation problem from FS recon? It seems that there is no quick answer on fixing the aparc+aseg? Thank you, p On Tue, Oct 11, 2011 at 10:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I'll have to refer you back to the freesurfer list for that one. There are people with much more expertise than me on troubleshooting the recon-all stream. Once you get your recons fixed, you'll have to rerun all trac-all steps except 1.1 (image corrections). On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: The original aparc+aseg are not good, at least for these two cases. So which parameters in recon-all should be tweaked? On Tue, Oct 11, 2011 at 5:38 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Is the original aparc+aseg from the freesurfer recon not good either (from mri/aparc+aseg.mgz)? Or is it messed up only after registration into diffusion space (dlabel/diff/aparc+aseg.flt.nii.gz, dlabel/diff/aparc+aseg.bbr.nii.gz)? This will determine if the freesurfer recon needs to be fixed or if the registration needs to fixed. On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: yeap, the aparc+aseg_masks are not good. Any way to fix this? Thanks. On Tue, Oct 11, 2011 at 5:00 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I see, the mask may be the answer to the initialization failures! It seems like the fmajor you sent me also has its endings masked out? That'd cause it to fail. I wish I'd thought of this earlier! With usemaskanat = 1, the mask that's used is a slightly dilated version of the aparc+aseg from the FS recon, mapped to diffusion space. So if the aparc+aseg has those parts missing, or if the diffusion-anatomical registration is not good, parts will be masked out that shouldn't. The anatomical mask can be found in dlabel/diff/aparc+aseg_mask* (if you've run both flirt and bbregister registrations, there'll be 2 of them). Does this mask look like something went wrong? On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: I used the default, i.e. set usemaskanat =1, but it looks that tracts were not reconstructed at the place where it was masked out (see the cross-bar at L_unc.png). I still have no luck in fixing the initialization issue (see fmajor.png for example). Thanks. On Tue, Oct 11, 2011 at 3:19 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - If you're using the anatomical brain as a mask (set usemaskanat = 1, which is the default), then the diffusion-based mask won't have an effect on your outputs. BTW, have you had any luck with your initialization issues? Sorry I haven't had another chance to look at your data since we last emailed, I got bogged down with some other stuff. a.y On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: Hi Anastasia, I'd like to lower the bet threshold value by set thrbet = 0.01 for skull-stripping because some of the brains have been cut, but it does not seem to make any changes (see attached). Any suggestion? Thank you,
[Freesurfer] FreeSurfer Questions
Dear FreeSurfer Gurus, We are looking for a way to normalize the intensity histogram for our subjects. In the past we have used Brain Image Java, using FSL-Fast inhomogeneity corrections. Unfortunately we are unable to open the output files (.img, .hdr) in FreeSurfer. When trying to import the files (after converting them to nii) we get a talaraich error: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) here is the mri_info for a subject we get this error with: Volume information for S029_nii type: nii dimensions: 256 x 256 x 100 voxel sizes: 0.9375, 0.9375, 1.5000 type: SHORT (4) fov: 240.000 dof: 0 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -75.0, zend: 75.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0. : x_a = 0., y_a = 1., z_a = 0., c_a = 0. : x_s = 0., y_s = 0., z_s = 1., c_s = 0. Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -0.9375 0. 0. 120. 0. 0.9375 0. -120. 0. 0. 1.5000 -75. 0. 0. 0. 1. voxel-to-ras determinant -1.31836 ras to voxel transform: -1.0667 0. 0. 128. -0. 1.0667 -0. 128. -0. -0. 0.666750. 0. 0. 0. 1. We are either looking to get the files we currently have to import correctly in FreeSurfer, or import our DICOM files into a program and normalize the intensity histogram and output a file freesurfer can read. We are looking to get rid of hyper intensities in the temporal and frontal lobes that cause main and pial surface errors. Thanks for whatever help you can give, now and in the future. Chris McCarthy ___ 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] FreeSurfer Questions
Hi Christopher try outputing nifti from FSL instead of analyze and see if that helps. Don't go through analyze at all. cheers, Bruce On Wed, 19 Oct 2011, Christopher McCarthy wrote: Dear FreeSurfer Gurus, We are looking for a way to normalize the intensity histogram for our subjects. In the past we have used Brain Image Java, using FSL-Fast inhomogeneity corrections. Unfortunately we are unable to open the output files (.img, .hdr) in FreeSurfer. When trying to import the files (after converting them to nii) we get a talaraich error: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) here is the mri_info for a subject we get this error with: Volume information for S029_nii type: nii dimensions: 256 x 256 x 100 voxel sizes: 0.9375, 0.9375, 1.5000 type: SHORT (4) fov: 240.000 dof: 0 xstart: -120.0, xend: 120.0 ystart: -120.0, yend: 120.0 zstart: -75.0, zend: 75.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = 0. : x_a = 0., y_a = 1., z_a = 0., c_a = 0. : x_s = 0., y_s = 0., z_s = 1., c_s = 0. Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -0.9375 0. 0. 120. 0. 0.9375 0. -120. 0. 0. 1.5000 -75. 0. 0. 0. 1. voxel-to-ras determinant -1.31836 ras to voxel transform: -1.0667 0. 0. 128. -0. 1.0667 -0. 128. -0. -0. 0.6667 50. 0. 0. 0. 1. We are either looking to get the files we currently have to import correctly in FreeSurfer, or import our DICOM files into a program and normalize the intensity histogram and output a file freesurfer can read. We are looking to get rid of hyper intensities in the temporal and frontal lobes that cause main and pial surface errors. Thanks for whatever help you can give, now and in the future. Chris McCarthy ___ 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] trac-all results
Glad things are moving in the right direction. Now it looks like maybe one of the control points of the path is not moving around, which is why you get that very bright thin spot in the distribution. I can't tell by looking at that one slice of the mask only, but could it be that there voxels missing from the mask around there? If so you could fill them in and try again. You can also overlay the path.pd on the FA map and check if that part is off the white matter or on its edge. On Wed, 19 Oct 2011, Ping-Hong Yeh wrote: The mask sort of covers the whole brain (see attached). It may be due to the display thresholding, when I viewed the path.pd.nii.gz using fslview, the tract actually has been recovered as compared to the previous one (old_path.png). However, the path.pd still does seem normal, i.e. with quite a few extraordinary high intensity (probability, yellow)? Thanks. ping On Wed, Oct 19, 2011 at 2:52 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Do the corresponding brain masks in diffusion space (dlabel/diff/aparc+aseg_mask.bbr.nii.gz and aparc+aseg_mask.flt.nii.gz) now cover the entire brain well, after the aparc+aseg fixes? a.y On Tue, 18 Oct 2011, Ping-Hong Yeh wrote: Hi Anastasia, I got fixed of the aparc+aseg (see aparc+aseg.png) in one of problematic data and re-ran the trac-all following your suggestions. However, the segmented forceps major using FLIRT still not getting good result (see flt.png) though BBR one is OK (see bbr.png). Similarly the segmented L CST using BBR looks weird, but the ones using FLIRT seem OK. It appear the problems are not simply due to the poor segmentation from the T1 recon-all. Any further suggestions? BR, Ping On Fri, Oct 14, 2011 at 11:04 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping-Hong, Yes, you can set usemaskanat = 0 in your dmrirc, and then the brain mask will be extracted from the DWI data by the bet tool, instead of using the aparc+aseg. But, and this is a big but, TRACULA uses the aparc+aseg to constrain the tractography solutions, i.e. the aparc+aseg is where the UnderLying Anatomy in TRACULA comes from. So the quality of the trac-all results depend on the quality of the aparc+aseg regardless of where your mask came from. a.y On Fri, 14 Oct 2011, Ping-Hong Yeh wrote: Hi Anastasia, Can trac-all just use the mask in diffusion native space (by setting usemaskanat = 0? ) so I get around the T1 segmentation problem from FS recon? It seems that there is no quick answer on fixing the aparc+aseg? Thank you, p On Tue, Oct 11, 2011 at 10:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I'll have to refer you back to the freesurfer list for that one. There are people with much more expertise than me on troubleshooting the recon-all stream. Once you get your recons fixed, you'll have to rerun all trac-all steps except 1.1 (image corrections). On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: The original aparc+aseg are not good, at least for these two cases. So which parameters in recon-all should be tweaked? On Tue, Oct 11, 2011 at 5:38 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Is the original aparc+aseg from the freesurfer recon not good either (from mri/aparc+aseg.mgz)? Or is it messed up only after registration into diffusion space (dlabel/diff/aparc+aseg.flt.nii.gz, dlabel/diff/aparc+aseg.bbr.nii.gz)? This will determine if the freesurfer recon needs to be fixed or if the registration needs to fixed. On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: yeap, the aparc+aseg_masks are not good. Any way to fix this? Thanks. On Tue, Oct 11, 2011 at 5:00 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I see, the mask may be the answer to the initialization failures! It seems like the fmajor you sent me also has its endings masked out? That'd cause it to fail. I wish I'd thought of this earlier! With usemaskanat = 1, the mask that's used is a slightly dilated version of the aparc+aseg from the FS recon, mapped to diffusion space. So if the aparc+aseg has those parts missing, or if the diffusion-anatomical registration is not good, parts will be masked out that shouldn't. The anatomical mask can be found in dlabel/diff/aparc+aseg_mask* (if you've run both flirt and bbregister registrations, there'll be 2 of them). Does this mask look like something went wrong? On Tue, 11 Oct 2011, Ping-Hong Yeh wrote: I used the default, i.e. set usemaskanat =1, but it looks that tracts were not reconstructed at the place where it was masked out (see the cross-bar at L_unc.png). I still have no luck in fixing the initialization issue (see fmajor.png for example). Thanks. On Tue, Oct 11, 2011 at 3:19 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - If you're using the anatomical brain as a mask (set usemaskanat = 1, which is the default), then the diffusion-based mask won't have an effect on your outputs. BTW, have you had any luck with
Re: [Freesurfer] Group Average of Retinotopy Results
Hi Michelle, try this: isxconcat-sess -sf sessidlist -a rtopy.fsaverage.lh -call -o retgroup cd retgroup/rtopy.fsaverage.lh mri_glmfit --y eccen/ces.000.nii.gz --osgm --o eccen/glm.real --surface fsaverage lh mri_glmfit --y eccen/ces.001.nii.gz --osgm --o eccen/glm.imag --surface fsaverage lh mri_glmfit --y polar/ces.000.nii.gz --osgm --o polar/glm.real --surface fsaverage lh mri_glmfit --y polar/ces.001.nii.gz --osgm --o polar/glm.imag --surface fsaverage lh mri_fieldsign --fs lh.fieldsign.mgh \ --eccen eccen/glm.real/osgm/gamma.mgh eccen/glm.imag/osgm/gamma.mgh \ --polar polar/glm.real/osgm/gamma.mgh polar/glm.imag/osgm/gamma.mgh \ --s fsaverage --hemi lh --sphere --old tksurfer fsaverage lh inflated -aparc -ov lh.fieldsign.mgh -fthresh .5 Michelle Umali wrote: Hi Doug and the Freesurfers, Thanks for your help. I have 2 questions.: 1) I did the retinotopy analysis on the fsaverage surface as you suggested below and then ran isxconcat-sess for my eccen and polar data: e.g. isxconcat-sess -analysis rtopy.fsaverage.lh -contrast polar -sf sessid -o group_polar_lh but how do you do this for the fieldsign analysis, since the cess.nii and other files don't exist? 2) So when trying to run a group mri_glmfit on the polar and eccen maps with: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh --glmdir group_eccen_lh.wls --nii.gz I got an error, because I have two ces.nii.gz and cesvar.nii.gz files each. I am not sure how this happened. I only have one run each of polar and wedge data. What may have generated these two files and which one do I use? Thanks. Michelle On Thu, Oct 13, 2011 at 11:36 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: When you run preproc-sess use -surface fsaverage lhrh instead of -surface self lhrh. Then create a new analysis with the same parameters, except use -surface fsaverage lh instead of -surface self lh. doug Michelle Umali wrote: Hi Doug, I'm a little confused as to how to assign functional data to the fsaverage space. 1) Do you mean just change each subject's subjectname file to fsaverage and then do the same thing as before for each person? 2) Also, when I specify the analysis do I change -rtopy.self.lh to rtopy.fsaverage.lh, i.e. will isconcat later be sensitive to analysis name? e.g. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force then the same for selxavg3-sess and fieldsign-sess and then isxconcat-sess would be: isxconcat-sess -sf sessid -analysis rtopy.fsaverage.lh -o group_lh Thanks. Michelle On Wed, Oct 12, 2011 at 3:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: If you want to combine across subjects, then you need to run the analysis on fsaverage (ie, rerun preproc-sess, create a new analysis, run selxavg3-sess, and then isxconcat-sess). doug Michelle Umali wrote: Dear Freesurfers, I've generated individual polar, eccentricity, and fieldsign maps for each of my subjects. I would like to generate group average maps of these that I can visualize on the fsaverage brain. When I ran: isxconcat-sess -sf sessid -analysis rtopy.self.lh -o group_lh I got: ERROR: analysis space is self surface, not supported How do I do a group average for the 3 different maps? Thanks. Michelle For each person I ran recon-all and flattened occipital patches. Then: mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sjXX -fsd bold -force selxavg3-sess -a rtopy.self.lh -s sjXX -force selxavg3-sess -a rtopy.self.rh -s sjXX -force fieldsign-sess -a rtopy.self.lh -occip -fwhm 20 -s sjXX fieldsign-sess -a rtopy.self.rh -occip -fwhm 20 -s sjXX
Re: [Freesurfer] Group Average of Retinotopy Results
Hi Doug, Thank you for your help with this. So when I looked at the maps, two issues arose. 1) The fieldsign map looks like it needs lots of smoothing. When I ran the individual subjects on the surface, I smoothed by 20 during fieldsign-sess. Is it still appropriate/can one smooth at the mri_fieldsign step below? 2)Results ended up on the lateral side and way anterior from the occipital lobe. Do I perform a separate registration between the individual subject and fsaverage somewhere along the line? Is this because I ran the individual subject analyses on a flattened fsaverage occipital patch and not on lh.sphere? Thanks! Michelle On Wed, Oct 19, 2011 at 7:34 PM, Michelle Umali mumal...@gmail.com wrote: Hi Doug, Two problems happened (I'm attaching a picture). 1) The fieldsign map looks like it needs lots of smoothing. When I ran the individual subjects on the surface, I smoothed by 20 during fieldsign-sess. Is it still appropriate/can one smooth at the mri_fieldsign step below? 2)Results ended up on the lateral side and way anterior from the occipital lobe. Do I perform a separate registration between the individual subject and fsaverage somewhere along the line? Is this because I ran the individual subject analyses on a flattened fsaverage occipital patch and not on lh.sphere? Thanks! Michelle On Wed, Oct 19, 2011 at 5:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Michelle, try this: isxconcat-sess -sf sessidlist -a rtopy.fsaverage.lh -call -o retgroup cd retgroup/rtopy.fsaverage.lh mri_glmfit --y eccen/ces.000.nii.gz --osgm --o eccen/glm.real --surface fsaverage lh mri_glmfit --y eccen/ces.001.nii.gz --osgm --o eccen/glm.imag --surface fsaverage lh mri_glmfit --y polar/ces.000.nii.gz --osgm --o polar/glm.real --surface fsaverage lh mri_glmfit --y polar/ces.001.nii.gz --osgm --o polar/glm.imag --surface fsaverage lh mri_fieldsign --fs lh.fieldsign.mgh \ --eccen eccen/glm.real/osgm/gamma.mgh eccen/glm.imag/osgm/gamma.mgh \ --polar polar/glm.real/osgm/gamma.mgh polar/glm.imag/osgm/gamma.mgh \ --s fsaverage --hemi lh --sphere --old tksurfer fsaverage lh inflated -aparc -ov lh.fieldsign.mgh -fthresh .5 Michelle Umali wrote: Hi Doug and the Freesurfers, Thanks for your help. I have 2 questions.: 1) I did the retinotopy analysis on the fsaverage surface as you suggested below and then ran isxconcat-sess for my eccen and polar data: e.g. isxconcat-sess -analysis rtopy.fsaverage.lh -contrast polar -sf sessid -o group_polar_lh but how do you do this for the fieldsign analysis, since the cess.nii and other files don't exist? 2) So when trying to run a group mri_glmfit on the polar and eccen maps with: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh --glmdir group_eccen_lh.wls --nii.gz I got an error, because I have two ces.nii.gz and cesvar.nii.gz files each. I am not sure how this happened. I only have one run each of polar and wedge data. What may have generated these two files and which one do I use? Thanks. Michelle On Thu, Oct 13, 2011 at 11:36 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: When you run preproc-sess use -surface fsaverage lhrh instead of -surface self lhrh. Then create a new analysis with the same parameters, except use -surface fsaverage lh instead of -surface self lh. doug Michelle Umali wrote: Hi Doug, I'm a little confused as to how to assign functional data to the fsaverage space. 1) Do you mean just change each subject's subjectname file to fsaverage and then do the same thing as before for each person? 2) Also, when I specify the analysis do I change -rtopy.self.lh to rtopy.fsaverage.lh, i.e. will isconcat later be sensitive to analysis name? e.g. mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force then the same for selxavg3-sess and fieldsign-sess and then isxconcat-sess would be: isxconcat-sess -sf sessid -analysis rtopy.fsaverage.lh -o group_lh Thanks. Michelle On Wed, Oct 12, 2011 at 3:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: If you want to combine across subjects, then you need to run the analysis on fsaverage (ie, rerun preproc-sess, create a new analysis, run selxavg3-sess, and then isxconcat-sess). doug Michelle Umali wrote: Dear Freesurfers, I've generated individual polar, eccentricity, and fieldsign
[Freesurfer] Subcortical segmentation atlas
Hello, I am working on comparing hand-drawn subcortical volumes to those output automatically by FreeSurfer. While reading about the segmentation process on the wiki, I came across this line: The final segmentation is based on both a subject-independent probabilistic atlas and subject-specific measured values. The atlas is built from a training set, i.e., a set of subjects whose brains (surfaces or volumes) have been labeled by hand. These labels are then mapped into a common space (Talairach space for volumes... (http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview) Because of the way we decided to delineate our ROI, we need to compare the shapes we defined in AFNI to those defined by this training set and output by FreeSurfer. I've been looking for more information about this probabilistic atlas, but I cannot find any more information about it. The only thing I found was the last line of this thread from the mail archives: Am 23.08.2011 um 04:03 schrieb Anthony Dick: The subcortical segmentation identifies subcortical structures such as thalamus, basal ganglia structures, hippocampus, amygdala, and cerebellum. The cortical parcellation delineates different areas of the cortex, such as the superior temporal sulcus, the central sulcus, the pars triangularis, opercularis, and orbitalis of the inferior frontal gyrus. A recommendation is to get a copy of the Duvernoy atlas, which covers definitions of different parts of the cortex. The Mai atlas is good for learning subcortical structures. Was the Mai atlas used to create the define the structures in the training set? Could you provide me with any more information regarding the training set? ___ 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] Subcortical segmentation atlas
no, we created our own atlas by manually labeling 39 subjects according to the CMA conventions, then iteratively going back over them to correct for consistent inaccuracies in the manual labelings. It's still an ongoing process as we are currently working on improving the manual putamen labels. cheers Bruce On Wed, 19 Oct 2011, cloud.c...@me.com wrote: Hello, I am working on comparing hand-drawn subcortical volumes to those output automatically by FreeSurfer. While reading about the segmentation process on the wiki, I came across this line: The final segmentation is based on both a subject-independent probabilistic atlas and subject-specific measured values. The atlas is built from a training set, i.e., a set of subjects whose brains (surfaces or volumes) have been labeled by hand. These labels are then mapped into a common space (Talairach space for volumes... (http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOvervie w) Because of the way we decided to delineate our ROI, we need to compare the shapes we defined in AFNI to those defined by this training set and output by FreeSurfer. I've been looking for more information about this probabilistic atlas, but I cannot find any more information about it. The only thing I found was the last line of this thread from the mail archives: Am 23.08.2011 um 04:03 schrieb Anthony Dick: The subcortical segmentation identifies subcortical structures such as thalamus, basal ganglia structures, hippocampus, amygdala, and cerebellum. The cortical parcellation delineates different areas of the cortex, such as the superior temporal sulcus, the central sulcus, the pars triangularis, opercularis, and orbitalis of the inferior frontal gyrus. A recommendation is to get a copy of the Duvernoy atlas, which covers definitions of different parts of the cortex. The Mai atlas is good for learning subcortical structures. Was the Mai atlas used to create the define the structures in the training set? Could you provide me with any more information regarding the training set? ___ 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.
