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Re: [Freesurfer] longitudinal processing, template and flags
by Daniel Ferreira 31 Jan '14

31 Jan '14

Thanks Martin for your reply, I am agree with you on point 1. What would you say in the case that we are interested in rates of decline from baseline to 12 months, but besides 6 months follow-up we also have 24 months?. Here I see more conceptual problems. In an hypothetical context of severe atrophy from 12 to 24 months, adding the 24 mo follow-up perhaps difficult registration more than improves it. What do you think? Thanks a lot Best Daniel Hi Daniel, 1. yes. But why not include 6 month in your study if you have those scans??? You will get much more reliable slope estimates with 3 time points compared to 2, so including that time point will not only help for the image processing part, but also in your statistics (you gain power). 2. I am not familiar with the mprage flag and think it mainly affects the normalization. If you are sure you need it, then also add it to the -base and -long runs, just to be safe. best, Martin On 01/29/2014 09:08 AM, Daniel Ferreira wrote: Dear experts, I have two questions regarding the longitudinal stream: - I am including Baseline and 12 months follow-up in my study. However, I also have 6 months follow-up. I wonder if it is conceptually right to include these 6 months scans in template creation with the idea of increasing registration. - I am applying the -mprage flag in the crossectional first step. Should I use it in the -base and -longs steps too? Thanks very much Daniel Ferreira

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-hemi flag and control points
by silver47＠gmx.com 30 Jan '14

30 Jan '14

Hi, If control points are only added to one hemisphere, is it ok to use the -hemi flag together with -autorecon2-cp -autorecon3 for recon-all? Thanks, P

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tksurfer overlay color range control bug report
by Joseph Dien 30 Jan '14

30 Jan '14

Hi, I’m using FreeSurfer 5.3.0 on OS X 10.9.1. I seem to have run into a GUI bug. When I go to Configure Overlay Display and change the Min setting the display range changes appropriately on the figure once I press the Apply button. When I change the max setting (e.g., from 5 to 50) the Histogram changes appropriately when I press Apply (the green line moves to 50) but nothing changes on the figure. Furthermore, if the color scale is displayed, the scale ends are unchanged (still 5). If I press Close and then open it up again the Max is no longer changed (still 5) and the Histogram now displays the unchanged value (green line at 5). If, however, I change the Max by right-clicking then not only does the histogram change (without needing to press Apply) but also the figure once I press Apply. Cheers! Joe Cut-and-paste the following info into your FreeSurfer problem report: --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 13.0.0 x86_64 --------------------------------------------------------------------- Please include the following additional information in your report: 1) tksurfer overlay color range control bug report 2) tksurfer fsaverage lh inflated -aparc -overlay AP1-fusiform-voxel-ST-FacSF1lh.nii.gz 3) none 4) not relevant See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting which tksurfer /Applications/freesurfer/bin/tksurfer -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist Maryland Neuroimaging Center University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com

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Re: [Freesurfer] Longitudinal RepeatedMeasuresAnova mri_glmfit "--surf subject hemi"
by Martin Reuter 30 Jan '14

30 Jan '14

Hi Kaiming, 1. Depends on what you are interested in (atrophy per month or yearly rate , select 1 or 2). To include age I'd make a column with age at baseline or mean age of the subject's time points, not time varying. I have no clue what you are looking at, but the significance maps should not change . But you really don't have a analysis here anyway with only one subject! So who knows what's going on. 2. Usually people look at thickness or volume. Selecting area or area_mm grabs those columns from the stats files. I have no idea what the difference is . Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Kaiming Yin <yinkaiming6987(a)gmail.com> Date:01/30/2014 6:21 PM (GMT-05:00) To: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Cc: FreeSurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Longitudinal RepeatedMeasuresAnova mri_glmfit "--surf subject hemi" Hi Martin, Thanks for the help of glm, I also try the QDEC table for the 3 times points of 1 same subject k. k was scanned at Aug-2012, May-2013, and Jul-2013. A little confusion here is should I record the time as which one of these: (1) --time years (2) --time months (3) --time ages 0 0 25.36 0.77 9 26.13 0.92 11 26.28 I used these three timing ways and find that the freeview overlay shreshold differ a lot. both the (1) --time years and (3) --time ages can use threshold range as 2, 5 which i think means p<0.01 and p>0.00001? but the (2) --time months fits the threshold only as 0.1, 0.5 (p<0.8 and p>0.3?). The shape of the histogram are all the same in all these three and the area covered are also the same. In the tutorial I see the example use the first timing way, i.e. --time years, which also use the threshold as 2,5. Another question is when I call the long_stats_slopes command: long_stats_slopes --qdec long.qdec.table.dat --stats aseg.stats --meas Area_mm2 --do-avg --do-rate --do-pc1 --do-spc --do-stack --time ages --sd ../.. long_stats_slopes --qdec long.qdec.table.dat --stats lh.aparc.stats --meas area --do-avg --do-rate --do-pc1 --do-spc --do-stack --time ages --sd ../.. the flag --meas uses two different but very similar measures for area, and not sure what is the difference there. Thanks a lot, Kaiming On Thu, Jan 30, 2014 at 6:46 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Kaiming, thickness is not a surface, it is a function defined on a surface. Don't add it as a surface name to the command line. Best, Martin On 01/30/2014 11:12 AM, Kaiming Yin wrote: Dear Martin, Make sense now. thanks for this. Yes I only have one subject with 3 different time points, what about the longitudinal two stage model (QDEC)? will this work? and one more question about the glm is when doing the thickness comparison, calling the mri_glmfit command, should I mention: mri_glmfit ... --surf fsaverage lh thickness? or just left it as ... --surf fsaverage lh? I saw the default <surfacename> is 'white'. But when I add this 'thickness' parameter it seems can not work either and reports like: " gdfReadHeader: reading rmanova.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 TP1-vs-TP2 0 0.816497 1 TP1-vs-TP3 0 0.816497 Class Means of each Continuous Variable 1 k 0.0000 0.0000 INFO: gd2mtx_method is doss Reading source surface /Freesurfer//k/surf/lh.thickness nquads=5767172, nvertices=569 ERROR: MRISread: file '/Freesurfer//k/surf/lh.thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface! Invalid argument " Thanks for your patience, Kaiming On Thu, Jan 30, 2014 at 3:46 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Dear Kaiming, how many subjects do you have? only 1? You need to have more data to run a glm (your degrees of freedom is 0 , see error message). Your other question: you can select any target for running your analysis. But usually people do not select one of the subjects from the study, because that may introduce a processing bias towards that subject (maybe the thickness changes of that subject will drive the results or bias it). That is why fsaverage is recommended. Best, Martin On 01/30/2014 06:13 AM, Kaiming Yin wrote: Dear Martin, Yes I think so, and I run the mri_glmfit with fsaverage as the subject like: mri_glmfit --glmdir lh.thickness.rmanova --y lh.thickness.sm05.mgh --fsgd rmanova.fsgd doss --C tp1-vs-tp2.mtx --C tp1-vs-tp3.mtx --C tp2-vs-tp3.mtx --C tp-effect.mtx --C mean.mtx --surf fsaverage lh it reports: FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Freesurfer/k/lh.thickness.sm05.mgh logyflag 0 usedti 0 FSGD rmanova.fsgd labelmask /Freesurfer//fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.thickness.rmanova IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.thickness.rmanova Loading y from /Freesurfer/k/lh.thickness.sm05.mgh INFO: gd2mtx_method is doss Saving design matrix to lh.thickness.rmanova/Xg.dat Normalized matrix condition is 1.73205 Matrix condition is 1.73205 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 149955 voxels in mask Saving mask to lh.thickness.rmanova/mask.mgh Reshaping mriglm->mask... search space = 74612.965197 DOF = 0 ERROR: DOF = 0 It seems still something wrong was ignored. Also if I call the preproc or surf2surf commands with the base subject, i.e. k, instead of fsaverage, will it work? or even better? mris_preproc --target k --hemi lh --meas thickness --out lh.thickness.mgh --fsgd rmanova.fsgd mri_surf2surf --s k --hemi lh --fwhm 5 --sval lh.thickness.mgh --tval lh.thickness.sm05.mgh Thanks, Kaiming On Thu, Jan 30, 2014 at 3:18 AM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Your data was probably mapped to fsaverage when you call the preproc or surf2surf commands? If so you should specify fsaverage as the subject nane. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Kaiming Yin Date:01/29/2014 9:07 PM (GMT-05:00) To: FreeSurfer Mailing List Subject: [Freesurfer] Longitudinal RepeatedMeasuresAnova mri_glmfit "--surf subject hemi" Dear FreeSurfer guys, I am using longitudinal processing stream and with the RepeatedMeasuresAnova. I follow the instruction here from http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova my fsgd file is: GroupDescriptorFile 1 Title k_longitudinal Class k Variables TP1-vs-TP2 TP1-vs-TP3 Input k_1 k 1 1 Input k_2 k -1 0 Input k_3 k 0 -1 contrasts is: tp1-vs-tp2.mtx tp1-vs-tp3.mtx tp2-vs-tp3.mtx tp-effect.mtx mean.mtx 0 1 0 0 0 1 0 -1 1 0 1 0 1 0 0 0 0 1 I run the mris_preproc and mri_surf2surf commands as the same for left hemi thickness, but when I run the mri_glmfit command it reports "ERROR: you must use '--surface subject hemi' with surface data". if i add the flag as: mri_glmfit ...(as the same before)... --surface k lh or --surface k lh thickness or --surface k_1.long.k lh or --surface k_1.long.k lh thickness or --surface k_1 lh or --surface k_1 lh thickness it still goes wrong and even not make an output folder. Any problems there? thanks, Kaiming 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. -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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transferring annotation from one subject to another
by Marie Schaer 30 Jan '14

30 Jan '14

Hi all, I have an annotation for fsaverage that I would like to convert into a subject's space. Up to now, the only way I found to do that was to convert my annotation to all its labels, and then rebuilt the annotation in the subject's space from the labels, using the following 3 steps mri_annotation2label --annotation myAparc --hemi ?h --subject fsaverage --outdir fsaverage/label/ mri_label2label --srcsubject fsaverage --srclabel fsaverage/label/?h.label1.label --trgsubject SUBJ --regmethod surface --hemi ?h --trglabel SUBJ/label/?h.label1.label (which needs to be repeated for each label) mris_label2annot --ctab myColorLUT.txt --l ?h.label1.label [ … up to --?h.labelX.label] --s SUBJ --a myAparc --hemi ?h That is however not really efficient for annotations including increasing numbers of labels. Is there any other way to convert more efficiently the annotation, something like an annotation2annotation command? Thanks a lot in advance for your answer, Marie

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Re: [Freesurfer] Longitudinal RepeatedMeasuresAnova mri_glmfit "--surf subject hemi"
by Martin Reuter 30 Jan '14

30 Jan '14

Your data was probably mapped to fsaverage when you call the preproc or surf2surf commands? If so you should specify fsaverage as the subject nane. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Kaiming Yin <yinkaiming6987(a)gmail.com> Date:01/29/2014 9:07 PM (GMT-05:00) To: FreeSurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Longitudinal RepeatedMeasuresAnova mri_glmfit "--surf subject hemi" Dear FreeSurfer guys, I am using longitudinal processing stream and with the RepeatedMeasuresAnova. I follow the instruction here from http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova my fsgd file is: GroupDescriptorFile 1 Title k_longitudinal Class k Variables TP1-vs-TP2 TP1-vs-TP3 Input k_1 k 1 1 Input k_2 k -1 0 Input k_3 k 0 -1 contrasts is: tp1-vs-tp2.mtx tp1-vs-tp3.mtx tp2-vs-tp3.mtx tp-effect.mtx mean.mtx 0 1 0 0 0 1 0 -1 1 0 1 0 1 0 0 0 0 1 I run the mris_preproc and mri_surf2surf commands as the same for left hemi thickness, but when I run the mri_glmfit command it reports "ERROR: you must use '--surface subject hemi' with surface data". if i add the flag as: mri_glmfit ...(as the same before)... --surface k lh or --surface k lh thickness or --surface k_1.long.k lh or --surface k_1.long.k lh thickness or --surface k_1 lh or --surface k_1 lh thickness it still goes wrong and even not make an output folder. Any problems there? thanks, Kaiming

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glmfit - matrix is ill-conditioned or badly scaled
by Linda Zhang 30 Jan '14

30 Jan '14

Dear all, Whilst running mri_glmfit, the following error occurred: ERROR: matrix is ill-conditioned or badly scaled, condno = 12375.1 I've attached the design matrix, the fsgd file, and one of the contrast matrices as an example. The command line was: mri_glmfit --glmdir lh.all.thickness.glmdir --y lh.thickness.10.mgh --fsgd all.fsgd dods --C allavovsallcvo.mtx --C avovscvo.mtx --C mavovsavo.mtx --C mavovsmcvo.mtx --C mcvovscvo.mtx --surf fsaverage lh --cortex What should I change? Cheers, Linda

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longitudinal processing, template and flags
by Daniel Ferreira 30 Jan '14

30 Jan '14

Dear experts, I have two questions regarding the longitudinal stream: - I am including Baseline and 12 months follow-up in my study. However, I also have 6 months follow-up. I wonder if it is conceptually right to include these 6 months scans in template creation with the idea of increasing registration. - I am applying the -mprage flag in the crossectional first step. Should I use it in the -base and -longs steps too? Thanks very much Daniel Ferreira

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Re: [Freesurfer] freeview porblem under ubuntu 12.04
by Ruopeng Wang 30 Jan '14

30 Jan '14

This looks like graphics driver issue. Is your graphics card driver up-to-date? Is there any error/warning message in the console? Ruopeng On 01/30/2014 01:17 PM, Markus Gschwind wrote: > HI Ruopeng, > > Here it is. > > Is it related to the tbouble shoot I did for trackvis? > > Thanks for having a look, > Markus > > > 2014-01-30 Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu > <mailto:rpwang@nmr.mgh.harvard.edu>> > > Can you post a screenshot? > > Ruopeng > > > On 01/30/2014 12:58 PM, Markus Gschwind wrote: >> Dear Experts, >> >> I have installed Freesurfer 5.3 under ubuntu 12.04. >> >> It is running fine except for Freeview which is causing heavy >> graphic trouble (thousands of colored squares in the black fields >> where the brains should be displayed. >> >> Tksurfer is working fine. >> >> Glxgears is showing the rotating blue, red and green gears. >> >> There is no error in the terminal. >> >> What could I do to track down the problem? >> >> Thanks for help! >> Markus >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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. > >

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parcellation of grey and white matter is incorrect across large portions of the cortex
by Christine Smith 30 Jan '14

30 Jan '14

Hello, The parcellation of grey and white matter appears to be off in several T1-weighted structural scans I have been processing. The effect is observed in the temporal lobes, parietal lobes, and part of the occipital lobes. The frontal lobe does not seem to be affected as much. For example, the medial white matter is super white, while more distal white matter near the cortex is less white (grey). Grey matter itself is rather dark (black in some cases). If you monkey around with the brightness of the image you can see that, for example, the pial line has actually followed the distal white matter and not the grey matter. Moreover, the white matter line has followed the boundary between medial (super white) white matter and more distal (greyer) white matter. This effect is most pronounced in the temporal and parietal lobes nearest the brightest parts of the white matter across the entire scan. About 3-5 voxels are cut off. For the frontal lobe and caudal occipital lobe, though, it is only cutting off about 1 voxel around the edge of the brain. I have attached a picture of this problem with the pial and white matter lines on the image. Look at the cortex in the lower left hand part of the image (lateral temporal cortex). For the image called Missing_Voxels.tiff I have adjusted the standard brightness of the image in freesurfer to show how much of the brain we are missing. In the image called Missing_Voxels_Brighter.tiff I have left the brightness levels as they appear when you open freesurfer. The problem appears less severe in this latter image because the standard brightness level has made some of the grey matter appear black and it is easier to miss that it is actually present. Now look at the top of the image and see that the pial line there is pretty accurate, though it does appear to cut off maybe 1 voxel too much. Extracting the eTIV from one of these scans shows that their intracranial volume is much smaller than other participants whose data were obtained on a different scanner. Also, each lobe volume is reduced. For example, the parietal lobe is about 15 standard deviations smaller than a group of participants scanned on a different scanner. These types of reductions are observed if you include grey matter only and also if you include grey+white matter in the calculation of the lobe volumes. Thus, the problem appears to be that we are missing the most outer part of the grey matter across a large part of the brain. I should also mention that the skull itself is missing (on the T1 image) near the lateral temporal lobes so there may be some signal dropout there. Though the lateral temporal cortex itself becomes visible when the brightness of the scans is adjusted, the skull in that area never does become visible. Is there any way to fix this problem at a basic level in one of the earlier steps of freesurfer? I have tried putting in a bunch of control points in the "real" white matter and it does make the white matter extend out further. However, the pial line is still cutting off ~3-4 voxels of brain in the problematic areas. Best, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego

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