Re: [Freesurfer] Mri_concat: initial frame ok but noisy in output image
Hi, Thank you for your help! I think there might be something wrong just with the display, as in fact more brains looked strange. I have re-run the concatenation with the same commands after killing many processes on my computer and now all brains look correct and in the expected order. Cheers, Aga On 7/19/11 10:19 PM, "Douglas N Greve" wrote: > > > Hi Aga, that does sound strange. mri_concat does no processing at all, > so if that subject looks ok before you run mri_concat, it should look > fine afterwards. Try running just that subject through mri_concat (so > there's no real concatenation). Also, make sure that the bad subject in > the mri_concat output is the same subject that you are looking at > individually; you could be off by 1. > > doug > > Agnieszka Burzynska wrote: >> >> Dear experts, >> I used mri_concat to concatenate sig.mgh files from fixed-level >> analysis (combining runs within each subject). All input files when >> viewed as initial single frame images look correct. For one person, >> however, in the multiframe image the sig.mgh looks just like noise >> (see attached picture). I used only --i and --o in the mri_concat >> command line. What could have happened? I get no error messages and >> everything else looks ok. >> >> Thank you for your help, >> Aga >> >> >> >> >> ___ >> 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] Calculating ROI size from label, min ROI size
Dear all, I have 2 questions: 1) I created labels for some ROIs on fsavgerage (qdec analysis). I got statistics from these rois for each individual subject (by map-to-subjects, etc.), but what I am now interested in is to know the size of the ROI on the group level (so on the fsaverage surface). Following up on the recent post, I tried 'mris_curvature_stats' but it gives error if I dont specify the subject. I am not to familiar with different commands, perhaps there is another one that would work? 2) Is there any "golden standard" for the minimum p-value or minimum size of an ROI to be considered a significant finding? I expect this may differ quite a lot, depending on how strong the effects of a variable on cortical thickness can be expected. Still, if you could comment on this or refer me to some literature, I would be very grateful. Thank you a lot, Best regards, Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Label sizes, min ROI size
Dear experts, I have 2 questions: 1) I created labels for some ROIs on fsavgerage (qdec analysis). I got statistics from these rois for each individual subject (by map-to-subjects, etc.), but what I am now interested in is to know the size of the ROI on the group level (so on the fsaverage surface). Following up on the recent post, I tried 'mris_curvature_stats' but it gives error if I dont specify the subject. I am not to familiar with different commands, perhaps there is another one that would work? 2) Is there any "golden standard" for the minimum p-value or minimum size of an ROI to be considered a significant finding? I expect this may differ quite a lot, depending on how strong the effects of a variable on cortical thickness can be expected. Still, if you could comment on this or refer me to some literature, I would be very grateful. Thank you a lot! Best regards, Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Label sizes, min ROI size
Dear Doug, Thank you for your reply! The command results in ERROR: Option --slabel unknown. I could not figure it out from the options descriptions with other option i could use, so i need some help again... Cheers & thank you! Aga On 9/14/09 7:48 PM, "Douglas N Greve" wrote: > > Try something like this > > mri_segstats --slabel fsaverage lh path/to/lh.yourlabel.label --sum > lh.yourlabel.sum > > The 4th column of the summary file will have the Area in mm^2 > > doug > > Agnieszka Burzynska wrote: >> Dear experts, >> I have 2 questions: >> >> 1) I created labels for some ROIs on fsavgerage (qdec analysis). I got >> statistics from these rois for each individual subject (by map-to-subjects, >> etc.), but what I am now interested in is to know the size of the ROI on the >> group level (so on the fsaverage surface). >> >> Following up on the recent post, I tried 'mris_curvature_stats' but it gives >> error if I dont specify the subject. I am not to familiar with different >> commands, perhaps there is another one that would work? >> >> 2) Is there any "golden standard" for the minimum p-value or minimum size of >> an ROI to be considered a significant finding? I expect this may differ >> quite a lot, depending on how strong the effects of a variable on cortical >> thickness can be expected. Still, if you could comment on this or refer me >> to some literature, I would be very grateful. >> >> Thank you a lot! >> Best regards, >> Aga >> >> ___ >> 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
[Freesurfer] FSL and freesurfer: combine runs in volume or on surface?
Dear all, I am trying to figure out how to bring my fMRI data from FSL to the freesurfer surface. The way I understood it from the tutorial "3.0 Surface-based Group Functional Analysis"( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat) There are two possibilities of combining multiple runs per subject: - using mris_preproc for each run and having runs as frames in the lh.copex.mhg file - running first gfeat in FSL and registering gfeat copes to fsaverage ( Runs combined in a GFEAT within a Subject), which would result in 1-frame lh.copex.mhg file I wonder if it is possible to say which procedure is better/more sensitive? Should the fmri data be non-smoothed before this step for both above options? Thank you! Cheers, Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] average p-value from an ROI
Dear all,
I have a follow-up question to the previous discussion ("correction for
behavioral varialbles in qdec" Tue, 04 Aug 2009.
Is there an option to extract the average p-value from a ROI? After a group
analysis I specified ROIs at p < 0.001 and extracted the mean cortical
thickness, the peak p-value, and mean ROI size. Now, I would like to report
not the peak, but the average p-value of an ROI in the fsaverage space. Is
there any flag to obtain this information? I did not use the mri_surfcluster
command, but a matlab script to extract the information form the output of
the mri_segstats command.
Thanks for help!
Cheers,
Aga
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Re: [Freesurfer] reg-feat2anat: a problem!
Dear Doug, Thank you a lot! Our feat data is always nifti, but anatomical FSL data is sometimes in the analyze format. Is this already a problem? I will now check the rest. Thank you, cheers, Aga On 2/7/11 4:35 PM, "Douglas N Greve" wrote: > Hi Aga, are you using nifti? If analyze, that could be the problem. Do > your functionals and anatomicals have a different sign to their > determinants (you can check with mri_info). In principle, reg-feat2anat > should handle this but in some cases it does not. The 5.1 version will > handle it properly. If they do have the same sign, then look through the > log file and find the flirt command. Run that command by itself (you may > need to run reg-feat2anat with --nocleanup to keep it from deleting the > files). If that fails, then contact the FSL people > > doug > > Agnieszka Burzynska wrote: >> Dear all, >> I am using the command reg-feat2anat to transform functional data >> pre-processed in FSL to the anatomical image in Freesurfer. >> >> As suggested, I check the registration with reg-feat2anat --feat >> run2.feat manual. >> >> I have 3 runs of functional data for each subject. Surprisingly, some >> runs are registered well but others not (even of the same subject, so >> using the same reference anatomical images: see the attached image. >> Upper row: bad registration of one run and lower row: good >> registration of another run). >> >> I have no problem to manually correct the registrations, it works >> well, but as I have many subjects, I wonder if there may be a way to >> change some options of reg-feat2anat to make it work better? Can you >> see from the attached image what is the problem with my images? (I >> viewed the functional and anatomical data of a few subjects, some woth >> good and some with bad registration and see no difference or flip) >> >> Thanks a lot for your help! >> Aga >> >> >> >> >> >> ___ >> 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] autorecon1 after Talairach correction: can I re-run other than with -notalairach?
Dear all, For one of my subjects I had to correct the Talairach step manually. My manual correction, however, may not be perfect. Is it possible to re-run autorecon1 using the Talairach correction to GUIDE (but not REPLACE) the automatic registration? Thank you! Aga ___ 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] fMRI data from FSL into Freesurfer: is my workflow correct?
Dear Doug, Thank you a lot for your reply! Yes, I did use reg-feat2anat and registered example_func to the subject's anatomical. As far as I understand it, then the registration matrix can be used for a contrast of interest. That's great news that the software version will not be a problem. I will use the copes, thank you. My cope images have a range of, for example, -500 to 500 with the peak at 0. When I view them on the subject anatomical in the freesurfer (with command tkmedit 1109 orig.mgz lh.white -aux brain.mgz -overlay ./run1.feat/stats/cope1.nii.gz -overlay-reg ./run1.feat/reg/freesurfer/anat2exf.register.dat -segmentation aparc+aseg.mgz -fthresh 2.3 -fmax 4.3 ), the -fthresh 2.3 and -fmax 4.3 are not suitable. However, when I try to adjust the threshold in View/Configure/Functional Overlay I get this error message: Invalid values. Tkmedit couldn't set the threshold to the values you specfied. Please make sure the minimum is less than or equal to the midpoint, and the slope is greater than 0. I am not sure how to deal with this. Now the last point: >> - I will want to create a fMRI-based ROI and then investigate the >> thickness especially within this region. i know I can extract mean ROI >> values and use other statistical software, but how can I perform >> vertex-wise analysis within this ROI? I assume qdec does not allow >> this, so only the DODDS analysis is possible. >> > Which stat map do you want to derive the ROI from? The group map? Yes, my first idea was to create a conjunction image across all subjects, specify the ROI on the fsaverage, then map this ROI back to subjects' individual surfaces. And then see whether across subjects, thickness is related to fmri data within this cortical patch. Thank you again for your help! Cheers, Aga On 5/10/11 4:39 PM, "Douglas N Greve" wrote: > Hi Aga, comments below > > Burzynska, Aga wrote: >> >> >> Dear all, >> I just wanted to double-check if I am doing the right thing. >> >> I am transferring fMRI data from FSL to the surface in Freesurfer to >> test whether cortical thickness is related to BOLD signal change. >> >> I used the steps described here: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer >> >> I did the following: >> 1) I carried out Freesurfer reconstruction for all subjects >> 2) I performed 1st level analysis for fMRI data in FSL, separately for >> each run, without smoothing >> 3) Then I obtained good registration of FEAT example_func of each run >> to the subject's anatomical using FLIRT. This I have done already for >> a specific contrast of interest. >> > Did you not use reg-feat2anat for this step? Did you register the z-map > itself? If so, that is not the right thing to do, it should be the > example_func. >> >> The above steps have been performed with Freesurfer version earlier >> than 5.0. Will there be a problme if I continue the steps below with >> the newest stable version? >> > This will not be a problem. >> >> Now I plan: >> 4) Combine the 3 runs/subject on the surface by averaging them with >> smoothing. As this is within-subject, my guess is that 5mm will be the >> best. >> > Sounds good. Make sure to use the copes and not the zstats >> >> 5) Concatenate the images for all subjects to perform analyses >> >> I am not sure about the following points: >> - what are the units of the zstat images transferred onto the surface? >> Is it still the logarithmic scale as for thickness analyses? >> > I'm not sure what you mean. As I mention above, you should use the copes > and not the zstats for the next higher level analysis. >> >> - I will want to create a fMRI-based ROI and then investigate the >> thickness especially within this region. i know I can extract mean ROI >> values and use other statistical software, but how can I perform >> vertex-wise analysis within this ROI? I assume qdec does not allow >> this, so only the DODDS analysis is possible. >> > Which stat map do you want to derive the ROI from? The group map? > > doug > >> >> Thank you a lot for your support! >> Best, >> Aga >> >> >> >> >> ___ >> 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] fMRI data from FSL into Freesurfer: is my workflow correct?
Dear Doug, Thank you again very much for your help. I am replying with a delay because I was travelling. Please see my questions& comments below in the text: On 5/10/11 5:48 PM, "Douglas N Greve" wrote: > > > Agnieszka Burzynska wrote: >> Dear Doug, >> Thank you a lot for your reply! >> >> Yes, I did use reg-feat2anat and registered example_func to the subject's >> anatomical. As far as I understand it, then the registration matrix can be >> used for a contrast of interest. >> >> That's great news that the software version will not be a problem. >> >> I will use the copes, thank you. >> >> My cope images have a range of, for example, -500 to 500 with the peak at 0. >> When I view them on the subject anatomical in the freesurfer >> >> (with command tkmedit 1109 orig.mgz lh.white -aux brain.mgz -overlay >> ./run1.feat/stats/cope1.nii.gz -overlay-reg >> ./run1.feat/reg/freesurfer/anat2exf.register.dat -segmentation >> aparc+aseg.mgz -fthresh 2.3 -fmax 4.3 >> ), >> >> the -fthresh 2.3 and -fmax 4.3 are not suitable. However, when I try to >> adjust the threshold in View/Configure/Functional Overlay I get this error >> message: >> >> Invalid values. >> Tkmedit couldn't set the threshold to the values you specfied. Please make >> sure the minimum is less than or equal to the midpoint, and the slope is >> greater than 0. >> > What are you trying to adjust them to? I tried to apply some meaningful threshold, otherwise the whole brain is yellow-blue. However, so far the zstats (as you refer to them bewlo) look ok, so I may use zstats, given our later analyses. >> I am not sure how to deal with this. >> >> Now the last point: >> >>>> - I will want to create a fMRI-based ROI and then investigate the >>>> thickness especially within this region. i know I can extract mean ROI >>>> values and use other statistical software, but how can I perform >>>> vertex-wise analysis within this ROI? I assume qdec does not allow >>>> this, so only the DODDS analysis is possible. >>>> >>>> >>> Which stat map do you want to derive the ROI from? The group map? >>> >> >> Yes, my first idea was to create a conjunction image across all subjects, >> specify the ROI on the fsaverage, then map this ROI back to subjects' >> individual surfaces. And then see whether across subjects, thickness is >> related to fmri data within this cortical patch. >> > If you are going to create a conjunction, then you should use the > zstats. But then you have another problem in that the zstats are going > to be very low because no smoothing was done. But if you're happy with > the maps, then go for it. Alternatively, you can do a group analysis of > the copes and then threshold the sig maps. In either case, the map will > be in the fsaverage space. You can create a label in tksurfer. Then run > mri_preproc to get all of your subjects thickness files into one file in > fsaverage space. Then run mri_segstats using the --slabel and --avgwf > options with the thickness file as input. The avgwf file will be a list > of thicknesses for each subject averaged over the ROI. > > doug I plan to apply smoothing on the surface when averaging the 3 runs for each subjects, so I hope zstats will look sufficiently good (I am still checking it). Concerning the ROI issue, if possible, I would NOT do the ROI-analysis. Instead, I am searching for a way to correlate the thickness with fMRI data across subjects (both data types are in fsaverage space). In other words, I have two images for each subject in the surface space: the thickness and some fmri measure. I would like to see how they are related vertex-wise within some larger regions of interest. It would be great if you could give me some guidance here, as I cannot find the solution in the archives or the tutorials. With best greetings, Aga >> Thank you again for your help! >> Cheers, >> Aga >> >> On 5/10/11 4:39 PM, "Douglas N Greve" wrote: >> >> >>> Hi Aga, comments below >>> >>> Burzynska, Aga wrote: >>> >>>> Dear all, >>>> I just wanted to double-check if I am doing the right thing. >>>> >>>> I am transferring fMRI data from FSL to the surface in Freesurfer to >>>> test whether cortical thickness is related to BOLD signal change. >>>> >>>> I used the steps described here: >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer >>&
[Freesurfer] Viewing a multi-frame image?
Dear all, I created a 3-frame image using a command similar to: mris_preproc --target fsaverage --hemi lh --fwhm 5 \ --out xrun/lh.cope1.mgh \ --iv fbert1.feat/stats/cope1.nii.gz fbert1.feat/reg/freesurfer/anat2exf.register.dat \ --iv fbert2.feat/stats/cope1.nii.gz fbert2.feat/reg/freesurfer/anat2exf.register.dat How can I view all 3 frames of the lh.cope1.mgh? I see just one frame with: tksurfer fsaverage lh inflated -overlay xrun/lh.cope1.mgh And don't know how to toggle between the frames. Thank you for your help! Cheers, Aga ___ 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] Viewing a multi-frame image?
Dear Doug, Yes, it works, thank you so much! Cheers, Aga On 7/7/11 3:57 PM, "Douglas N Greve" wrote: > Hi Aga, try View->Configure->Overlay. The config window will have a time > point entry at the top. > doug > > Agnieszka Burzynska wrote: >> Dear all, >> I created a 3-frame image using a command similar to: >> mris_preproc --target fsaverage --hemi lh --fwhm 5 \ >> --out xrun/lh.cope1.mgh \ >> --iv fbert1.feat/stats/cope1.nii.gz >> fbert1.feat/reg/freesurfer/anat2exf.register.dat \ >> --iv fbert2.feat/stats/cope1.nii.gz >> fbert2.feat/reg/freesurfer/anat2exf.register.dat >> >> >> How can I view all 3 frames of the lh.cope1.mgh? >> I see just one frame with: >> tksurfer fsaverage lh inflated -overlay xrun/lh.cope1.mgh >> And don't know how to toggle between the frames. >> >> Thank you for your help! >> >> Cheers, >> Aga >> >> >> >> ___ >> 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] DOF and smoothing in mri_glmfit
Dear all, I am combining 3 runs of a subject using fixed effects GLM and I wanted to make sure I am doing the right thing. For each subject I use: mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 , while lh.cope1.mgh contains the concatenated cope1 images of the same subject in fsaverage space (the same for varcope1). 1) Is it the right way? 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it correct? 3) The functional data has not been smoothed in the 1st level analysis in FSL (as recommended), and also not smoothed during sampling the copes to a common space. Therefore I want to smooth it here for the first time, but only with 5mm. Does it sound right? Cheers, Aga ___ 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] DOF and smoothing in mri_glmfit
Dear Doug, Thank you so much. I completely see you point, but I have re-run the 1st level feat without smoothing just because it has been recommended not to smooth in the volume and then transfer it onto the surface, but rather first smooth on the surface (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). What I plan to do in the end is to include the cortical thickness as the vertex-wise covariate in the functional group analysis. So the final analysis will be on the group level, where, as you say, the varcopes should not matter that much. However, I was also thinking of analyzing varcopes in addition to copes (group analysis) to relate the variance of BOLD signal to the thickness. Would you then recommend going back and taking the initial 1st level analysis with regular smoothing? Thank you! Aga On 7/7/11 4:43 PM, "Douglas N Greve" wrote: > Hi Aga, your commands look right. For the DOF, it should be the sum of > the DOFs from all the runs (probably won't make much of a difference). > Smoothing is a bit of an issue when you want to look at individual > results. Technically, you should smooth before you do the first level > analysis (ie, before your compute the varcope), but this would require > doing the FEAT analysis directly on surface data. Smoothing after > computing the varcope means that the varcope will not be accurate (it > will be too large). The penalty is that you will see less activation > than you should. At the group level, this is not such a big deal because > you're either not using the varcope or you are using it as a weight. > doug > > Agnieszka Burzynska wrote: >> Dear all, >> I am combining 3 runs of a subject using fixed effects GLM and I wanted to >> make sure I am doing the right thing. >> >> For each subject I use: >> mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof >> 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label >> $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 >> >> , while lh.cope1.mgh contains the concatenated cope1 images of the same >> subject in fsaverage space (the same for varcope1). >> >> 1) Is it the right way? >> 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it >> correct? >> 3) The functional data has not been smoothed in the 1st level analysis in >> FSL (as recommended), and also not smoothed during sampling the copes to a >> common space. Therefore I want to smooth it here for the first time, but >> only with 5mm. Does it sound right? >> >> Cheers, >> Aga >> >> ___ >> 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] Mri_glmfit ERROR: dimension inconsistency in source data
Hi, During running fixed effects glm to combine runs, the analysis of all but one subject went fine. The log file contains this error message: mri_surf2surf --srcsubject 1250 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 3runs/tmp.mris_preproc.63877/1250.1.mgh --sval 3runs/tmp.mris_preproc.63877/subjsurfvals.mgh --noreshape --no-cortex ERROR: dimension inconsistency in source data Number of surface vertices = 132315 Number of value vertices = 132299 I see that mri_vol2surf --src run1.feat/stats/varcope1.nii.gz --srcreg run1.feat/reg/freesurfer/anat2exf.register.dat --hemi lh --out 3runs/tmp.mris_preproc.63877/subjsurfvals.mgh --noreshape Results in creating a file with dimensions 132299 1 1. Which data source data has then 132315 vertices? How can I correct this? Thank you for your help! Best, Aga ___ 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] reg-feat2anat: correct anat2exf.register.dat only or also func2std?
Dear experts, I am using reg-feat2anat to register my functional data from FSL to anatomical and starndard space in Freesurfer. For some subjects the registration is bad. I can easily fix anat2exf.register.dat. However, as specified in reg-feat2anat help, I know that the registration failed as the func2std is incorrect, too. Is it enough to correct anat2exf.register.dat to correctly transfer functional data from feat to the surface space or do I also need to correct func2std? It seems to me that in the next steps I am using, such as sampling the functional data to fsaverage and further calculations in the fsaverage space do not rely on func2std. Is this correct? Cheers, Aga ___ 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] DOF and smoothing in mri_glmfit
Dear Doug, I wanted to follow up on our discussion: I have re-run the analysis with the smoothing during the 1st level analysis and indeed the activation pattern looks more as we expect from the 3D analysis in FSL, although the regions that are "active" are the same. Thank you for your advice! Best, Aga On 7/7/11 5:14 PM, "Agnieszka Burzynska" wrote: > Thank you! I think I will just try it out: now run it as it is but also run > the 1st level with smoothing, as I need to add some contrasts anyway. Then I > should also know the difference between volume and surface smoothing. > Cheers, > Aga > > On 7/7/11 5:07 PM, "Douglas N Greve" wrote: > >> The problem with doing the smoothing at the first level in FEAT is that >> it will be volume-based, not surface-based. I'm not sure what to tell >> you about using the varcopes. They will certainly be very noisy without >> smoothing, so probably smoothing is a good idea, even if it's volume-based. >> >> doug >> >> Agnieszka Burzynska wrote: >>> Dear Doug, >>> Thank you so much. I completely see you point, but I have re-run the 1st >>> level feat without smoothing just because it has been recommended not to >>> smooth in the volume and then transfer it onto the surface, but rather first >>> smooth on the surface >>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). >>> >>> What I plan to do in the end is to include the cortical thickness as the >>> vertex-wise covariate in the functional group analysis. >>> >>> So the final analysis will be on the group level, where, as you say, the >>> varcopes should not matter that much. >>> >>> However, I was also thinking of analyzing varcopes in addition to copes >>> (group analysis) to relate the variance of BOLD signal to the thickness. >>> >>> Would you then recommend going back and taking the initial 1st level >>> analysis with regular smoothing? >>> >>> Thank you! >>> Aga >>> >>> On 7/7/11 4:43 PM, "Douglas N Greve" wrote: >>> >>> >>>> Hi Aga, your commands look right. For the DOF, it should be the sum of >>>> the DOFs from all the runs (probably won't make much of a difference). >>>> Smoothing is a bit of an issue when you want to look at individual >>>> results. Technically, you should smooth before you do the first level >>>> analysis (ie, before your compute the varcope), but this would require >>>> doing the FEAT analysis directly on surface data. Smoothing after >>>> computing the varcope means that the varcope will not be accurate (it >>>> will be too large). The penalty is that you will see less activation >>>> than you should. At the group level, this is not such a big deal because >>>> you're either not using the varcope or you are using it as a weight. >>>> doug >>>> >>>> Agnieszka Burzynska wrote: >>>> >>>>> Dear all, >>>>> I am combining 3 runs of a subject using fixed effects GLM and I wanted to >>>>> make sure I am doing the right thing. >>>>> >>>>> For each subject I use: >>>>> mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof >>>>> 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label >>>>> $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 >>>>> >>>>> , while lh.cope1.mgh contains the concatenated cope1 images of the same >>>>> subject in fsaverage space (the same for varcope1). >>>>> >>>>> 1) Is it the right way? >>>>> 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it >>>>> correct? >>>>> 3) The functional data has not been smoothed in the 1st level analysis in >>>>> FSL (as recommended), and also not smoothed during sampling the copes to a >>>>> common space. Therefore I want to smooth it here for the first time, but >>>>> only with 5mm. Does it sound right? >>>>> >>>>> Cheers, >>>>> Aga >>>>> >>>>> ___ >>>>> 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] ERROR: dimension inconsistency in source data
Hi, I am sorry to re-post this problem, but I cannot find the source of my problem: During sampling the feat data to fsaverage using for example: mris_preproc --target fsaverage --hemi lh --out 3runs/lh.cope1.mgh --iv run1.feat/stats/cope1.nii run1.feat/reg/freesurfer/anat2exf.register.dat --iv run2.feat/stats/#cope1.nii run2.feat/reg/freesurfer/anat2exf.register.dat --iv run3.feat/stats/cope1.nii run3.feat/reg/freesurfer/anat2exf.register.dat For one subject I get in the log file: ... mri_surf2surf --srcsubject 1250 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval 3runs/tmp.mris_preproc.13727/1250.1.mgh --sval 3runs/tmp.mris_preproc.13727/subjsurfvals.mgh --noreshape --no-cortex ERROR: dimension inconsistency in source data Number of surface vertices = 132315 Number of value vertices = 132299 ... Does it mean that the recon-all files are incompatible with the functional images? Can this stem from some manual editing of pial surface? Where should I search to spot the problem? Thank you a lot, Aga ___ 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.
