[Freesurfer] citation for FsFast
Hi Doug, What is your preferred citation for FsFast (used for resting-state)? I couldn't really find a clear answer in the Zotero library or mail archives. Thanks and happy holidays! Linda ___ 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] DODS design and demeaning
Dear Freesurfer experts, I would be very greatful if you could help me with three (probably basic) questions regarding an mri_glmfit design. For the design and contrasts I used FSGDF. I have a 2x2 factorial design with one covariate (age). I specified all four groups (A1B1, A1B2, A2B1, A2B2) and the covariate in one model, because I would like to test for the interaction between A and B (regressing out the effects of age). Age was demeaned using the mean of all subjects (i.e. of all 4 groups). My first question regards the contrasts: If, besides the interaction and main affects of A and B, I would like to assess the difference between individual groups, for example A1B1 - A1B2, is it okay to use the same model (1 -1 0 0 + further 0's for the age regressors); or should I make a new FSGDF containing only the subjects of group A1B1 and A1B2? My second question is associated with the first: If it is allowed to use the same model, how does freesurfer deal withdemeaning? Since I used the mean of all subjects to demean and not just of the subjects of for example A1B1 and A1B2. My third question regards the DODS/DOSS issue. I used DODS, because I do not believe the slopes of age by volume (or age by area/thickness) will be exactly parallel between groups. I tested this also be using contrasts of the age regressors, (for example using the contrast 0 0 0 0 1 -1 -1 1 for a AxBxage interaction) and indeed there are interactions with age in some brain areas. For thickness, they were FDR corrected still significant, for other measeurs the were not significant after correction, but that seems natural given the sample sizes. No I wondered whether it would suffice to use a DODS design (since slopes differ between groups) or whether I should stratify groups further for age (for example use two models, one for young subjects, on for old subjects). If the latter is the case, I would end up with very small samples, I am afraid. Thanking you in advance, Maaike___ 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] DODS design and demeaning
On 12/24/14 5:21 AM, maaike rive wrote: Dear Freesurfer experts, I would be very greatful if you could help me with three (probably basic) questions regarding an mri_glmfit design. For the design and contrasts I used FSGDF. I have a 2x2 factorial design with one covariate (age). I specified all four groups (A1B1, A1B2, A2B1, A2B2) and the covariate in one model, because I would like to test for the interaction between A and B (regressing out the effects of age). Age was demeaned using the mean of all subjects (i.e. of all 4 groups). My first question regards the contrasts: If, besides the interaction and main affects of A and B, I would like to assess the difference between individual groups, for example A1B1 - A1B2, is it okay to use the same model (1 -1 0 0 + further 0's for the age regressors); or should I make a new FSGDF containing only the subjects of group A1B1 and A1B2? It is a tricky question. You will get the same group means regardless of whether you combine all subjects or use a 2nd FSGD. The difference will be that you will have a much higher DOF if you combine them all. This means that the noise in the other subjects informs you about the noise in those two groups. If you can justify this, then you can leave them combined. If the 2nd model gives you the results you want, then reporting that would be a stronger scientific result. My second question is associated with the first: If it is allowed to use the same model, how does freesurfer deal withdemeaning? Since I used the mean of all subjects to demean and not just of the subjects of for example A1B1 and A1B2. The demeaning is also tricky. I would actually test whether there is an interaction between group and age. If there is no interaction, then I would re-run using a DOSS model in which case the demeaning won't make a difference. My third question regards the DODS/DOSS issue. I used DODS, because I do not believe the slopes of age by volume (or age by area/thickness) will be exactly parallel between groups. I tested this also be using contrasts of the age regressors, (for example using the contrast 0 0 0 0 1 -1 -1 1 for a AxBxage interaction) and indeed there are interactions with age in some brain areas. For thickness, they were FDR corrected still significant, for other measeurs the were not significant after correction, but that seems natural given the sample sizes. No I wondered whether it would suffice to use a DODS design (since slopes differ between groups) or whether I should stratify groups further for age (for example use two models, one for young subjects, on for old subjects). If the latter is the case, I would end up with very small samples, I am afraid. If there is no interaction in the areas that show up in your contrast of interest, then it is safe to use DOSS. If there are, then I don't think that stratifying them solves the problem. doug Thanking you in advance, Maaike ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] retinotopy in subject volumetric space
I don't think we have a tool to display the color wheel in a volume. FreeView might be able to do it. For the color wheel in tksurfer, you are looking at the angle file (one for eccen and one for polar), so you would map them. You can run mri_surf2vol something like mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject --hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject --hemi rh --fillribbon --merge vol.angle.mgz --o vol.angle.mgz doug On 12/18/14 1:24 PM, Benjamin Zimmerman wrote: I mean the individual's anatomical volumetric space. On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: What do you mean by the individual's volumetric space? The anatomical space or the functional space? On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote: Thanks for the advice. I thought I would like to use mri_surf2vol, but I am a little confused about the parameters and how they relate to what the retinotopy analysis outputs. To be explicit, I want to view the real.nii.gz and imag.nii.gz files in an individual's volumetric space. I can load these as overlays to the inflated surface using tksurfer subject hemisphere inflated. Then I can configure the overlay to use a color wheel color scale and display as complex to see the retinotopic mapping. I'm not sure how I would go about using mri_surf2vol to recreate this map in volumetric space. Should I just use real.nii.gz and imag.nii.gz as surfval? Where is the registration file outputted in a retinotopy analysis? Thank you for any more help that you can provide, Ben On Mon, Dec 15, 2014 at 3:26 PM, dgw dgwake...@gmail.com mailto:dgwake...@gmail.com mailto:dgwake...@gmail.com mailto:dgwake...@gmail.com wrote: Hi Ben, You should be able to map it back with mri_surf2vol. I haven't done this, but the wiki page looks fairly detailed: http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol HTH D On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com mailto:benjamin.zimmerm...@gmail.com wrote: Hi all, FsFast has an excellent individual retinotopy analysis that allows me to see phase data on the inflated surface of the brain. Is there a way to view the results of the retinotopy analysis in the subject's original volumetric space rather than on the subject's surface space? Thank you for any help, Ben ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Re: [Freesurfer] DODS design and demeaning
Hi Doug, Thank you for your quick response. Concerning question3, do you mean that if there is an interaction with age, it is all right to use DODS (without stratification)? Thanks, Maaike Date: Wed, 24 Dec 2014 15:31:53 -0500 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] DODS design and demeaning On 12/24/14 5:21 AM, maaike rive wrote: Dear Freesurfer experts, I would be very greatful if you could help me with three (probably basic) questions regarding an mri_glmfit design. For the design and contrasts I used FSGDF. I have a 2x2 factorial design with one covariate (age). I specified all four groups (A1B1, A1B2, A2B1, A2B2) and the covariate in one model, because I would like to test for the interaction between A and B (regressing out the effects of age). Age was demeaned using the mean of all subjects (i.e. of all 4 groups). My first question regards the contrasts: If, besides the interaction and main affects of A and B, I would like to assess the difference between individual groups, for example A1B1 - A1B2, is it okay to use the same model (1 -1 0 0 + further 0's for the age regressors); or should I make a new FSGDF containing only the subjects of group A1B1 and A1B2? It is a tricky question. You will get the same group means regardless of whether you combine all subjects or use a 2nd FSGD. The difference will be that you will have a much higher DOF if you combine them all. This means that the noise in the other subjects informs you about the noise in those two groups. If you can justify this, then you can leave them combined. If the 2nd model gives you the results you want, then reporting that would be a stronger scientific result. My second question is associated with the first: If it is allowed to use the same model, how does freesurfer deal withdemeaning? Since I used the mean of all subjects to demean and not just of the subjects of for example A1B1 and A1B2. The demeaning is also tricky. I would actually test whether there is an interaction between group and age. If there is no interaction, then I would re-run using a DOSS model in which case the demeaning won't make a difference. My third question regards the DODS/DOSS issue. I used DODS, because I do not believe the slopes of age by volume (or age by area/thickness) will be exactly parallel between groups. I tested this also be using contrasts of the age regressors, (for example using the contrast 0 0 0 0 1 -1 -1 1 for a AxBxage interaction) and indeed there are interactions with age in some brain areas. For thickness, they were FDR corrected still significant, for other measeurs the were not significant after correction, but that seems natural given the sample sizes. No I wondered whether it would suffice to use a DODS design (since slopes differ between groups) or whether I should stratify groups further for age (for example use two models, one for young subjects, on for old subjects). If the latter is the case, I would end up with very small samples, I am afraid. If there is no interaction in the areas that show up in your contrast of interest, then it is safe to use DOSS. If there are, then I don't think that stratifying them solves the problem. doug Thanking you in advance, Maaike ___ 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 The information in this e-mail is intended only for the person to whom it
Re: [Freesurfer] DODS design and demeaning
I did not mean that. If there is an interaction then there are issues of interpretation when comparing means (ie, offsets) since the comparison then depends on the value of the covariate. Eg, at age 70 there may be no difference in offsets, at age 50 there may be a positive, then negative at age 90. The way you have it set up the comparison will take place at the sample mean. These issues does not stop most of the community from doing this type of test. You can probably get it published, you just need to be clear what you are doing and what the limitations are. doug On 12/24/14 4:47 PM, maaike rive wrote: Hi Doug, Thank you for your quick response. Concerning question3, do you mean that if there is an interaction with age, it is all right to use DODS (without stratification)? Thanks, Maaike Date: Wed, 24 Dec 2014 15:31:53 -0500 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] DODS design and demeaning On 12/24/14 5:21 AM, maaike rive wrote: Dear Freesurfer experts, I would be very greatful if you could help me with three (probably basic) questions regarding an mri_glmfit design. For the design and contrasts I used FSGDF. I have a 2x2 factorial design with one covariate (age). I specified all four groups (A1B1, A1B2, A2B1, A2B2) and the covariate in one model, because I would like to test for the interaction between A and B (regressing out the effects of age). Age was demeaned using the mean of all subjects (i.e. of all 4 groups). My first question regards the contrasts: If, besides the interaction and main affects of A and B, I would like to assess the difference between individual groups, for example A1B1 - A1B2, is it okay to use the same model (1 -1 0 0 + further 0's for the age regressors); or should I make a new FSGDF containing only the subjects of group A1B1 and A1B2? It is a tricky question. You will get the same group means regardless of whether you combine all subjects or use a 2nd FSGD. The difference will be that you will have a much higher DOF if you combine them all. This means that the noise in the other subjects informs you about the noise in those two groups. If you can justify this, then you can leave them combined. If the 2nd model gives you the results you want, then reporting that would be a stronger scientific result. My second question is associated with the first: If it is allowed to use the same model, how does freesurfer deal withdemeaning? Since I used the mean of all subjects to demean and not just of the subjects of for example A1B1 and A1B2. The demeaning is also tricky. I would actually test whether there is an interaction between group and age. If there is no interaction, then I would re-run using a DOSS model in which case the demeaning won't make a difference. My third question regards the DODS/DOSS issue. I used DODS, because I do not believe the slopes of age by volume (or age by area/thickness) will be exactly parallel between groups. I tested this also be using contrasts of the age regressors, (for example using the contrast 0 0 0 0 1 -1 -1 1 for a AxBxage interaction) and indeed there are interactions with age in some brain areas. For thickness, they were FDR corrected still significant, for other measeurs the were not significant after correction, but that seems natural given the sample sizes. No I wondered whether it would suffice to use a DODS design (since slopes differ between groups) or whether I should stratify groups further for age (for example use two models, one for young subjects, on for old subjects). If the latter is the case, I would end up with very small samples, I am afraid. If there is no interaction in the areas that show up in your contrast of interest, then it is safe to use DOSS. If there are, then I don't think that stratifying them solves the problem. doug Thanking you in advance, Maaike ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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] Intersection of gray matter and white matter lines - Question
Hi! When looking through the brain scans, I've noticed that the lines outlining white matter intersect with lines outlining the gray matter. How do I fix this problem? Thanks, Christina ___ 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.
