[Freesurfer] Retinotopy Registration to Anatomical

tkregister2 help to figure this out but am still unsure how to register the polar and eccentricity data to the anatomical. Any help would be most appreciated. -Michelle Umali ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Retinotopy Registration to Anatomical

lle > Try using bbregister. > > Cheers > Bruce > > > > On Jul 31, 2011, at 6:54 PM, Michelle Umali wrote: > >> Dear Freesurfers, >> During my retinotopy analysis, I was getting very strange fieldsign >> data (blue and red speckles) and my polar and eccentrici

[Freesurfer] bbregister

] Hi Michelle Try using bbregister. Cheers Bruce On Jul 31, 2011, at 6:54 PM, Michelle Umali wrote: Dear Freesurfers, During my retinotopy analysis, I was getting very strange fieldsign data (blue and red speckles) and my polar and eccentricity data was limited to the occipital pole. It was

[Freesurfer] Bbregister & retinotopy

Dear Freesurfers, I've been troubleshooting my bizarre looking fieldsign data. I ran bbregister for my polar and eccentricity images, then re-ran the retinotopy analysis. The data still look the same. The fieldsign image is still a mass of blue and red speckles. Any tips on how I should p

[Freesurfer] troubleshooting retinotopy

Hi Freesurfers, I'm troubleshooting my retinotopy data and am still having issues with wonky fieldsign data. The registration looked ok, so now I am trying to look at the retinotopy results using rtview. I got an error message saying it can't find the register.dof6.dat file. So, now I am

Re: [Freesurfer] troubleshooting retinotopy

a, is it -map eccen? thanks. michelle Quoting Douglas N Greve : > How do the eccen and polar look by themselves? You can look at them > with tksurfer-sess > doug > > Michelle Umali wrote: >> Hi Freesurfers, >> I'm troubleshooting my retinotopy data and am still hav

[Freesurfer] Retinotopy trouble shooting

a, is it -map eccen? thanks. michelle Quoting Douglas N Greve : [Hide Quoted Text] How do the eccen and polar look by themselves? You can look at them with tksurfer-sess doug Michelle Umali wrote: Hi Freesurfers, I'm troubleshooting my retinotopy data and am still having issues with wonky

[Freesurfer] tksurfer and viewing eccentricity data

Dear Freesurfers, Is this the correct command for viewing eccentricity data using tksurfer: tksurfer-sess -a rtopy.self.lh -s sj09 -map eccen Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] tksurfer and viewing eccentricity data

s. The first time > point is eccen, the 2nd is polar. These are unmasked angles in radians > (I think). For masked use (masked by p<.01) > > tksurfer-sess -a rtopy.self.lh -s sj09 -map angle.masked > > To see the significance maps use > > tksurfer-sess -a rtopy.self.l

[Freesurfer] tksurfer & rtview

Dear Freesurfers, In an effort to figure out why my field sign data is a bunch of blue/red speckles, I looked at the polar and eccentricity maps separately on the surface. In both maps, I found that the values range from 0 to approximately 65. Does that seem to be OK, and if so, what do th

Re: [Freesurfer] tksurfer & rtview

d go from -pi to +pi. > What is you visualization command-line? You can change the color scale > from the View->Configure->Overlay window. > doug > > Michelle Umali wrote: >> Dear Freesurfers, >> >> In an effort to figure out why my field sign data is a bunch

[Freesurfer] tksurfer & rtview

Hi Doug, The z-values are consistently near or greater than 4. It just seems that the visualization of the angles is somehow incorrect... Is there be anything else that I need to check? Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.har

Re: [Freesurfer] tksurfer & rtview

oting Douglas N Greve : > Try smoothing (eg, -fwhm 5) when running fieldsign-sess. You can also > try using the sphere instead of the occip patch. > doug > > Michelle Umali wrote: >> Hi Doug, >> >> Thanks again for your advice, the heat maps look much better. Howev

[Freesurfer] tksurfer retinotopy analysis vs auto parcellation of V1/V2

. Michelle Alsouoting Douglas N Greve : > > > Michelle Umali wrote: >> Hi Doug, >> I've already smoothed by 5 during preproc-sess, so does this mean I >> should do additional smoothing during fieldsign-sess step? >> > Try the additional one now to see if it fix

[Freesurfer] tkmedit: Extending white matter and pial surfaces

Hi Freesurfers, When looking at the surfaces in tkmedit, I noticed that quite a bit of the tip of the temporal lobe was not included in pial/wm surfaces. I need to extend both surfaces. In what order does one do the edits? Does one paint in wm voxels first or pial first? Thanks. Michelle

[Freesurfer] Surface analysis FSL GFEAT results for multiple subjects with 4 runs each

Hi Freesurfers, I've been looking at the wiki for information on doing an surface analysis using GFEAT results for within subject, across multiple runs. On the wiki, a fixed effects analysis was used because there were only two runs. I have four runs and FSL uses FLAME 1 and FLAME 1+2. 1. Shoul

[Freesurfer] retinotopy description

Hi Freesurfers. Is there text describing the retinotopy analysis in Freesurfer mathematically? Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in t

[Freesurfer] tksurfer can't rotate hemisphere

Dear Freesurfers, I have recently installed Freesurfer 5.1 and FSL 4.1.4 on a linux machine. When I run tksurfer, I can't rotate the hemisphere. It will show the curvature, but the hemisphere just won't turn. I was able to do this through virtual box on my windows laptop. Is there another softwa

Re: [Freesurfer] tksurfer can't rotate hemisphere

acceleration under Ubuntu? Thanks. Michelle On Sun, Sep 25, 2011 at 1:16 PM, Bruce Fischl wrote: > nope, nothing else should be required. Did you push any "rotate" buttons > first? > > On Sun, 25 Sep 2011, Michelle Umali wrote: > > Dear Freesurfers, >> I have recentl

Re: [Freesurfer] tksurfer can't rotate hemisphere

pt. Something sounds like it is very wrong as it should be > less than a second, not a minute. You aren't running over vnc or something, > are you? > > > > On Sep 25, 2011, at 1:28 PM, Michelle Umali wrote: > > Dear Bruce and the Freesurfers, > > It turns out t

Re: [Freesurfer] tksurfer can't rotate hemisphere

nt angle make sure you hit return. Tk is strange > that way > > > > On Sep 25, 2011, at 1:50 PM, Michelle Umali wrote: > > Hi Bruce, > I got 28063 microseconds per iteration. No, I'm not running remotely. > Also, no matter what angle I choose, the rotation is always by 9

[Freesurfer] tksurfer rotation isssue

tksurfer in an email? I'm not sure what's > going on. When Nick/Krish/Ruopeng start reading email tomorrow, maybe they > can help > Bruce > > > > On Sun, 25 Sep 2011, Michelle Umali wrote: > > Hi Bruce, >> Pressing return after entering the angle doesn'

Re: [Freesurfer] tksurfer can't rotate hemisphere -SOLVED

Dear Bruce and the Freesurfers, I had to update my ATI graphics driver and set the doublebufferflag to 1. Everything is working just fine. Thanks for your help. Michelle On Sun, Sep 25, 2011 at 2:49 PM, Michelle Umali wrote: > Hi Bruce and the Freesurfers, > Sadly instead of .028 s

[Freesurfer] retinotopy analysis: tksurfer-sess dimension error between mask and surf

Dear Freesurfers, I am working on a retinotopy analysis and I got this error: ERROR: dimension mismatch between mask and surf when trying to look at map angle in tksurfer-sess Do I need to add --reshape flag? If so, where? Any help would be most appreciated. Thanks. Michelle Here are the analysi

Re: [Freesurfer] retinotopy analysis: tksurfer-sess dimension error between mask and surf

er 27, 2011, Douglas N Greve wrote: > Hi Michelle, did you change the structural after you ran the retinotopy analysis? It looks like the number of vertices changed. If so, then you'll need to re-run the fMRI analysis. > doug > > Michelle Umali wrote: >> >> Dear Freesurfer

[Freesurfer] Retinotopy tksurfer-sess: ERROR: mask and surf dimensions don't match

Hi Doug and Freesurfers I didn't change any of the structural After the retinotopy analysis. First, I ran recon-all -all. Second, I made edits to to brainmask.mgz and wm.mgz and then ran autorecon2-wm and autorecon3. Third, I cut the occipital patches in tksurfer and then flattened them. Finally,

[Freesurfer] fieldsign-sess: ERROR Surf/src mismatch

Dear Freesurfers, This is related to my retinotopy analysis tksurfer-sess dimension mismatch error message. So another subject had these errors come up during fieldsign-sess selxavg3-sess -a rtopy.self.lh -s sjXX -force (which ran without error) then I ran fieldsign fieldsign-sess -a rtopy.self.l

Re: [Freesurfer] fieldsign-sess: ERROR Surf/src mismatch

it run if you use > -sphere instead of -occip? > doug > > Michelle Umali wrote: >> >> Dear Freesurfers, >> This is related to my retinotopy analysis tksurfer-sess dimension >> mismatch error message. >> >> So another subject had these error

[Freesurfer] aseg2feat for PPI seeds for FSL

Hi Freesurfers, I want to do a PPI in FSL FEAT using the V1 left and righ found generated in recon-all as seeds using: I know for each subject I have to get a timecourse for my seeds fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz For each subject, I've run reg-feat2anat

Re: [Freesurfer] aseg2feat for PPI seeds for FSL

when doing setting up the PPI feat? Thanks. Michelle > > > Michelle Umali wrote: >> >> Hi Freesurfers, >> I want to do a PPI in FSL FEAT using the V1 left and righ found >> generated in recon-all as seeds using: >> >> I know for each subject I hav

[Freesurfer] fieldsign-sess: ERROR Surf/src mismatch

If everything is in synch, then it should print > make: Nothing to be done for `all'. > > If not, it should print out the steps that it would have run (if not for the > -dontrun option). > > doug > > Michelle Umali wrote: >> >> Hi Doug, >> I get the s

Re: [Freesurfer] fieldsign-sess: ERROR Surf/src mismatch

on-all -vno-check -s subject > This looks at the number of vertices in each of the surfaces to make sure > they are consistent. > > doug > > > Michelle Umali wrote: > >> Hey Doug and Freesurfers, >> At the bottom is the output showing what steps didn't run. &

[Freesurfer] aseg2feat and aparc2feat

Dear Freesurfers, I wanted to generate binary masks for areas found in the Freesurfer Color Lookup Table. For example, I wanted to use number 433, the Visual_V3d_l. I tried to use aseg2feat -feat featdir --aseg aparc+aseg fslmaths -featdir/reg/freesurfer/aparc+aseg.nii.gz -thr 433v uthr 433 \ f

[Freesurfer] aparc2feat and using Freesurfer Lookup Table

Dear Freesurfers, I wanted to generate binary masks for areas found in the Freesurfer Color Lookup Table. For example, I wanted to use number 433, the Visual_V3d_l. I tried to use aseg2feat -feat featdir --aseg aparc+aseg fslmaths -featdir/reg/freesurfer/aparc+ aseg.nii.gz -thr 433v uthr 433 \

[Freesurfer] Dimension Mismatch Error

Dear Freesurfers, I'm still getting a MRISripZeros() and MRIScopyMRI Surf/src mismatch error when running fieldsign-sess. You suggested that this problem was due to the surfaces being out of synch. When I ran recon-all -s subject -make all -dontrun, I saw that several steps had not run. The dat

Re: [Freesurfer] Dimension Mismatch Error

Hi Bruce, Will this undo my wm and pial edits? Thanks. Michelle On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl wrote: > try running > > > recon-all -s subject -make all > > and leave the -dontrun off. It should bring everything up to date > > Bruce > > > >

Re: [Freesurfer] Dimension Mismatch Error

anat should not have to be > re-run. > > doug > > Michelle Umali wrote: > >> Hi Bruce, >> Will this undo my wm and pial edits? >> >> Thanks. >> Michelle >> >> On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl >> > fis...@nmr.mgh.**harvar

Re: [Freesurfer] Dimension Mismatch Error

g.nii > polar/real.nii > polar/imag.nii > in the /usr/local/freesurfer/**subjects/retinotopy/sj12/bold/**rtopy.self.lh > directory? > > And the result of > mris_info /usr/local/freesurfer/**subjects/retinotopy/sj12/surf/** > lh.sphere > > doug > > > > >

[Freesurfer] reg-feat2anat: major failure

Hi Freesurfers, I've run reg-feat2anat to register my FSL FEAT data to the freesurfer anatomical data. And for most subjects the registration needs a little manual editing (which sometimes includes stretching). But for a few subjects, registration is terrible, e.g. coronal is switched with horizont

Re: [Freesurfer] Dimension Mismatch Error

ss it sees the anatomical directory. What else do you recommend? Thanks. Michelle On Mon, Oct 3, 2011 at 4:36 PM, Michelle Umali wrote: > Hi Doug, > I keep my retinotopy (sj) and anatomical (ld) data separate. I named the > retinotopy directory sj12 with the subjectname file says

[Freesurfer] upload issues for file drop

hi Freesurfers, I am trying to upload a 1.4 GB tgz file and I can't register as a new user through Accellion File Transfer. When I try uploading through regular File Drop, the connection times out (because the file is too big?). How can I upload this file? Thanks. Michelle __

[Freesurfer] Using Freesurfer reg-feat2anat registration to replace original FEAT

Dear Freesurfers, I've analyzed a run of functional data in FEAT and then used reg-feat2anat to register the FEAT results to the Freesurfer anatomicals. It turns out the original FLIRT registration was bad. When I looked at the reg-feat2anat results, images were flipped 90 degrees. I made edits

[Freesurfer] Major reg-feat2anat alignment issues along multiple axes

Hey Freesurfers, I've been trying to register my FEAT data to my Freesurfer data via reg-feat2anat in order to get V1 binary masks: reg-feat2anat --->aparc/aseg2feat --->fslmaths. It seemed to work ok, and I extracted time series for my areas of interest and ran a PPI analysis in FSL. When revi

[Freesurfer] warped flat occip patches and fieldsign maps

Dear freesurfers, I've been analyzing my retinotopy , have finally been able to run fieldsign-sess without running into dimension mismatch errors. Everything seemed ok until I tried looking at the fieldsign maps on flat patches. Some patches are warped with odd out of plane swirls. In others, al

[Freesurfer] retinotopy analysis description

Dear Freesurfers, I am trying to describe how freesurfer conducts it's retinotopy analysis to make the polar, eccen and fieldsign maps. Is there a detailed description of this somewhere? I can't seem to find an indepth description on the wiki. Thanks. Michelle

Re: [Freesurfer] warped flat occip patches and fieldsign maps

t; surfaces after flattening, so the flattening needs to be redone. The swirls > can be a number of things, possibly incorrect cuts. If you want to upload an > example I'll take a look. > > cheers > Bruce > > > > On Thu, 6 Oct 2011, Michelle Umali wrote: > > Dear f

[Freesurfer] selfreqavg

pic data analysis, especially in the endnotes of the article. also > for more details you can look at the MATLAB code embedded in the command > 'selfreqavg', which is used for the basic retinotopy analysis and is quite > readable. > > hope this helps, > > > -jon > >

[Freesurfer] Group Average of Retinotopy Results

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: an

[Freesurfer] Group Average of Retinotopy Results

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.fsaverag

[Freesurfer] rtview: trouble finding files

Dear Freesurfers, I know this is a very simple question. I'm just having trouble specifying the correct directories for rtview based on the example. When I run rtview, it can't find the image files that really do exist in the directory. For the following example in the help section: I did what I

[Freesurfer] reg-feat2anat failure

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

Re: [Freesurfer] reg-feat2anat failure

editing the registrations. Is there something I am doing wrong? Thanks. Michelle On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve wrote: > How are you generating the masks? > doug > > Michelle Umali wrote: > >> Hi Freesurfers, >> I've run reg-feat2anat on sever

Re: [Freesurfer] Group Average of Retinotopy Results

las N Greve 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, &g

Re: [Freesurfer] Group Average of Retinotopy Results

patch and not on lh.sphere? Thanks! Michelle On Wed, Oct 19, 2011 at 7:34 PM, Michelle Umali 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,

[Freesurfer] making a new label and binary mask

Hi Freesurfers, I would like to make a custom V1 and V2 label based on my fieldsign results and then later use aseg2feat and fslmaths to make binary masks based on this label to later use in an FSL feat analysis. I made the additions to a a modified (and differently named) version of each subject'

[Freesurfer] reg-feat2anat

Dear Freesurfers, I've previoiusly run reg-feat2anat on some fsl feat data, but now my advisor things i should re-preprocess my fsl data with a larger kernel size. Since it's the same dataset , do I have to re-run reg-feat2anat on this or can I just copy the registration folder from the old analys

[Freesurfer] when to invoke reg-feat2anat in fsl ppi

Dear Freesurfers, I am using seeds based on Freesurfer masks to run a PPI analysis and am wondering if I am using reg-feat2anat at the right fsl feat registration step. First, I ran an fsl analysis to generate a feat directory. Then I ran reg-feat2anat using that feat directory. Next I ran aseg2fe

[Freesurfer] rtview: ERROR cannot find eccen/real.nii

Dear All, I am still having trouble generating polar and eccen maps with rtview. I did this: cd $SUBJECTS_DIR/retinotopy/sj07/bold/rtopy.self.lh rtview.sh --s sj07 --lh --eccen \ --real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii The subjectname file is in $SUBJECTS_DIR/retinot

Re: [Freesurfer] rtview: ERROR cannot find eccen/real.nii

M, Douglas N Greve wrote: > Can you run it with --debug and send me the terminal output? > > Michelle Umali wrote: >> >> Dear All, >> I am still having trouble generating polar and eccen maps with rtview. >> >> I did this: >> cd $SUBJECTS_DIR

Re: [Freesurfer] rtview: ERROR cannot find eccen/real.nii

a-ha! I forgot to add .gz sorry for the silly error. thanks. michelle ___ 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

[Freesurfer] tksurfer crashes without error message

Hi Freesurfers, I've been using Freesurfer for a while, and have had no trouble with launching tksurfer. But recently I have tried to view an inflated hemisphere of a subject I have had no problem viewing before. The window no longer opens. This the case for all of my subjects, with whom I hav

Re: [Freesurfer] tksurfer crashes without error message

n Tue, Mar 20, 2012 at 8:43 AM, Bruce Fischl wrote: > Hi Michelle, > > hmmm, no idea. Do you want to upload the the subject and we'll see if we > can replicate the problem? Do you have enough memory on that machine? > > Bruce > > > > On Mon, 19 Mar 2012, Michelle U

[Freesurfer] masks from fsaverage label into Group FSL Feat

Hi Freesurfers, I've done a group feat analysis in FSL and I'd like to do an ROI analysis of V1/V2. I've also done recon-all on all my subjects. How would one generate the V1 and V2 binary masks from the fsaverage brain and then register it to the common MNI-152 brain used for the group feat analys

[Freesurfer] reg-feat2anat --feat --manxfm func2std

Hi Freesurfers, I ran reg-feat2anat and am now checking registration. For some subjects I had to edit the registration of feat to standard space. So, do I have to replace the example_func2standard.mat fsl's example_func2standard.mat in the reg folder or is this done automatically? Is this the onl

[Freesurfer] Please help: Registering to FSL feat- example_func2standard

Hi Freesurfers, I ran reg-feat2anat to register freesurfer data to FSL feat in order to generate some binary masks. Afterwards I edited the FEAT registration to standard space via: reg-feat2anat --feat subjectX.feat --manxfm func2std and saved the registration. i want to use these example_func2s

[Freesurfer] mri_gcut killed

Dear All, recon-all was killed during mri_gcut. Here is the error: mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz Killed. How does one deal with this? Thanks in advance for any help. Michelle ___ Freesurfer mailing list Freesurfe

[Freesurfer] retinotopy manual?

Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer. Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] retinotopy manual?

t; c. Display angle masked by by sig > tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked > d. Display field sign > tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign > > > > > > Michelle Umali wrote: >> Dear All, >> I was wondering if anyone

Re: [Freesurfer] retinotopy manual?

topy.self.lh -s sessid -map angle > c. Display angle masked by by sig > tksurfer-sess -a rtopy.self.lh -s sessid -map angle.masked > d. Display field sign > tksurfer-sess -a rtopy.self.lh -s sessid -fieldsign > > > > > > Mi

[Freesurfer] preproc-sess

Dear Freesurfers, I am still struggling with the retinotopy analysis. Whenever I try to run preproc-sess, I get this message: Session: /home/fsl/structural/LD08 Tue Apr 5 07:22:28 BST 2011 is not in SUBJECTS_DIR SUBJECTS_DIR is /home/fsl/structural I put the retinotopic

[Freesurfer] preproc-sess path structure

ake sure that your subjectname file has the name of the FreeSurfer > subject folder as found in $SUBJECTS_DIR (it looks like it is empty). > You don't need the retinotopy data in the $SUBJECTS_DIR. > doug > > Michelle Umali wrote: >> Dear Freesurfers, >> I am still stru

Re: [Freesurfer] preproc-sess path structure

ory, create a > text file called "subjectname". Put the subject name (ie, LD08-anat) > into the subjectname file. > > doug > > > > > > On 4/5/11 2:15 PM, Michelle Umali wrote: >> Hi Doug, >> Does the $SUBJECTS_DIR folder have to be where the FreeSur

[Freesurfer] Retinotopy-polar angle

Dear Freesurfers, I'm having issues trying to display the polar angle data using the color wheel. Unfortunately, I can't resizing the Configure Overlay Display window. No matter what I try, I can't actually see the Apply button. Any suggestions? Also, is there a quickie guide on defining th

Re: [Freesurfer] Retinotopy-polar angle

le, polar, and fieldsign info? Thanks very much. Michelle Quoting Douglas N Greve : > Michelle, > Can you give more details of what you are doing? How did you generate > the files you are trying to load? > doug > > Michelle Umali wrote: >> Dear Freesurfers, >> I

[Freesurfer] command line tksurfer

Hi Doug, I'm having issues with choosing the Color Wheel option inConfigure Overlay and not being able to see the Accept button (please see below). Can I change to Color Wheel via command line? thanks. Michelle __ I've been able to view the significance ma

[Freesurfer] tkmedit

Dear Freesurfers, I've noticed some problems in some inflated brains with the curvature displayed that I know will require manual intervention: -random spots of abnormally intense green or very intense red -tiny protrusions -falx cerebri obscuring parietal region -subcallosal splotches of red-gree

[Freesurfer] rtview and color bar

Hi Freesurfers! I ran rtview, and I couldn't find a color bar/legend. I'm just wondering how thow the colors get assigned. Is each color a position of wedge stimulus? I'm trying to define V1/V2/V3 boundaries and was wondering how to get the horizontal and vertical meridians. Any help wo

[Freesurfer] weird fieldsign image

Hi All, I am running a retinotopy analysis, and when I look at the fieldsign image all I see are a bunch of red and blue speckles. Is this normal? I am trying to figure out the horizontal and vertical meridians and am not sure how to use the fieldsign image to do this. It's for my thesis, i

[Freesurfer] fieldsign problems

Hi All, I am running a retinotopy analysis, and when I look at the fieldsign image all I see are a bunch of red and blue speckles. Is this normal? Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e

[Freesurfer] more on fieldsign problems-

Dear all, I've been having issues with my fieldsign images all I get are speckles. I did the following and did not get any errors: 1) ran recon-all -all 2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface 3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d

[Freesurfer] generating an amygdala mask

Dear Freesurfers, Is there a way to generate automatically generate an amygdala mask from recon-all results to fead into an FSL feat analysis? Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/

Re: [Freesurfer] more on fieldsign problems-

? There's no legend. Thanks. Michelle Quoting Douglas N Greve : > Hi Michelle, do the eccen and polar maps look ok? Also, I would > probably smooth them a little bit. The field sign calculation is > basically a spatial derivative so it can be sensitive to noise. > doug > &g