Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

visualize group analysis results of qdec
by Qijing Yu 25 Jun '14

25 Jun '14

Hello FreeSufers, I ran several analyses in qdec, and now have problem visualize previous analyses results...which sounds dumb... Please let me know if you have any ideas. I used fsaverage. I found this page http://freesurfer.net/fswiki/FsTutorial/Visualization using tksurfer, but it needs to do the "make_average". And it mentioned some "pre-computed results", I thought which would be the results of analyses via command line. Does this apply to the results by qdec? I also found the following command using Freeview: freeview -f SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d But I don't know which part of the command should I change. I tried the command as it is above anyway and the error is: Unrecognized sub-option flag 'annot_outline' Many thanks! All the best, Qijing

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Re: [Freesurfer] free-surfer longitudinal Qdec table
by Martin Reuter 25 Jun '14

25 Jun '14

Hi Anna I am not a statistician, but I would not control for duration separately, but rather use the time variable for that. It does not need to be in years (can be days out months). Measures closer in time are more correlated than measures further apart. Lme makes use of that information through the time variable. Best Martin Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Anna Jonsson <ajonsson09(a)gmail.com> Date:06/24/2014 11:52 AM (GMT+01:00) To: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Cc: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table thank you. and one other question; rather than putting years as the time variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut control for time between scans instead? On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Anna, whenever it says qdec-long the table is in qdec format (with a fsid-base as second column. It would then use the longitudinally processed results, which is what you want , both for lme and 2 stage model. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Anna Jonsson Date:06/09/2014 3:47 PM (GMT+01:00) To: Freesurfer support list Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table Hi, sorry for more questions, but i have a few. When running the first step of the lme implemented tools, doing the command mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh (assembles your thickness data into a single lh.thickness.mgh file), am I correct that this just needs to be a "normal" cross-sectional qdec table that free surfer subsequently makes into long format by --qdec-long option? so the lnogitudinal qdec table is only used in the two stage modell? This too just uses the cross-sectionally derived scans? Im confused where the .long runs become used? thank you and kind wishes On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Anna, Fsid is the cross sectionall name without the .long. Best martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Anna Jonsson Date:06/04/2014 7:22 AM (GMT-05:00) To: Freesurfer support list Subject: [Freesurfer] free-surfer longitudinal Qdec table Hi, I would like to make my freesurfer longitudinal qdec table for the to use in the lme matlab tools. However, does the fsid need to refer to the longitidunally derived subject; eg XXX.long, or the cross-sectionally derived subject, eg XXX. Im not sure based on the specification online. Kind Regards Anna _______________________________________________ Freesurfer mailing list Freesurfer(a)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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MatLab Version and Hardware and Freesurfer Statistics
by Gmail 24 Jun '14

24 Jun '14

Dear list, I am resending this message as I don’t know if it went through. Does the OS version, hardware or MatLab version (i.e., 2013a vs. 2014a) impacts in the results from the LME processing (Bernal-Rusiel et al.)? The LME is to be used for a Freesurfer 5.1/5.3 longitudinal pipeline. Regards, Pedro Rosa.

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Question regarding wm output
by Alejandra Machado 24 Jun '14

24 Jun '14

Hello! I'm a begginer user with this programm and i need some help, please! I was wondering if it's possible to get an output only for WM segmentation but excluding the filling in of CSF and/or hyperintensities? And if so, would it be possible to convert this to nii ? Thank you! Ale

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mkcontrast weighting a complicated double subtraction contrast
by DeCross, Stephanie N. 24 Jun '14

24 Jun '14

Hi, I’m having trouble figuring out the correct way to weight my conditions with mkcontrast for a couple of complicated contrasts I’m making. I have six conditions: #1 female face approach #2 male face approach #3 female face withdraw #4 male face withdraw #5 car approach #6 car withdraw For a couple of contrasts, I had to manually weight with -wcond. For this first one, everything worked. First I made an all faces (male and female, approaching or withdrawing) v. fixation (face_v_fix) contrast, weighted -a 1 -a 2 -a 3 -a 4. I then made an all cars (approaching or withdrawing) v. fixation (car_v_fix) contrast, weighted -a 5 -a 6. To make my contrast face_v_car, which is a subtraction of the above two contrasts, I used the command: mkcontrast-sess -contrast face_v_car -analysis 5.3loom_objns4runs.lh -ncond 6 -wcond 0.25 0.25 0.25 0.25 -0.5 -0.5. When I extracted the data in an ROI analysis for these three contrasts and a bunch others, I manually checked all ROI values for a given subject. The values for my face_v_fix and car_v_fix are correct, and when I manually subtract those two values, it gives me a value identical to the value that derives from the contrast itself. This is as it should be, as they’re two methods of computing the same thing. My problem is with a similar trio of contrasts. My contrast for all faces (both male and female) approaching minus all faces (male and female) withdrawing (aka face-aw), which is weighted -a 1 -a 2 -c 3 -c 4 in the mkcontrast command, and my car approaching minus car withdrawing contrast (aka car-aw), which is weighted -a 5 -a 6, are both fine. I’m trying to make a contrast face-aw minus car-aw (aka face-aw_v_car-aw), which essentially involves a double subtraction (faces approaching minus faces withdrawing, MINUS cars approaching vs. cars withdrawing) in which the face-aw part involves 4 conditions because of the two genders of faces but the car-aw part involves only 2. The command I used was: mkcontrast-sess -contrast face-aw_v_car-aw -analysis 5.3loom_objsns4runs.lh -ncond 6 -wcond 0.25 0.25 -0.25 -0.25 -0.5 0.5. When I extracted the ROI data, the values for my face-aw and car-aw contrasts were correct, but when I manually subtract them the value is different from the value that derives from the face-aw_v_car-aw contrast itself, when it should be equivalent. I have no idea why it’s not working. The only thing I can think that would affect this and mess it up is my weighting in the mkcontrast command. Do you know if I’m using the wrong weighting numbers or missing a flag I need or if there's some way to configure the contrast differently I should be doing? I’m sorry if I provided way more information than I needed to or not nearly enough; I’m very new at all things FreeSurfer and finding that the learning curve can be challenging. Thanks so much, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078

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Re: [Freesurfer] Longitudinal design
by Martin Reuter 24 Jun '14

24 Jun '14

HI Tudor, most of your questions are qdec or statistical questions, please post them to the Freesurfer list (with a different subject line) and maybe there is someone who can answer them. Lot's of people don't look at this mail, because it has 'Longitudinal" in it, but how many groups can be done in Qdec is a completely separate question. About the longitudinal aspect. If you do the 2-stage model, then you have thickness change as your dependent variable (instead of thickness in a cross sectional analysis). You can look at : - independent of group, where is thickness change different from zero. (or for each group separately). - You can compare groups, e.g. ask where is the change in thickness larger/smaller in one group vs the one of the other groups. For more complex modeling, I would recommend to include a biostatistician and run linear mixed effects models. The tools for that are available in FS53. Including thickness as a co-variate may be problematic. It may become tricky to interpret results (and there can very well be a coreallation with thickness change). If thickness changes as a percent, then you'll find a correlation with rate (as the same percent change in a thicker region is a larger rate in mm/time). If thickness changes more like an absolute (e.g. 0.2 mm/year) than in a thicker region the percent change will be smaller than in a thinner region. Best, Martin On Jun 15, 2014, at 3:56 PM, Tudor Popescu <tudor3(a)gmail.com> wrote: > Thanks! > > I'm a bit confused as to why designs with 4 or 6 groups can be analysed with QDEC (as per this FSGD examples page) whereas designs with 3 groups cannot be. It seems to me that an even number of groups is QDEC-able while an odd number isn't, but is there any workaround so that I can still use QDEC for my analyses? > > Since I'm guessing I might have to use mri_glmfit after all, I created a FSGD file (attached), with 3 groups and 9 variables (age + 8 behavioural measures indexing performance during and after the learning). I have subjects of both genders, but am not interested in gender effects - I just want to include gender in the model so as to control for the gender imbalance and "model out" variance caused by it. I'm guessing, though, that if in the contrasts, 1s and -1s are attributed based on group membership rather than gender, this should accomplish the purpose? Same thing goes for age, although it being continuous rather than categorical, it's easier conceptually. > > As I am not assuming different slopes for the different crossings of group and (age+behavioural predictors), I have built the FSGD as a DOSS. > > Some issues: > 1) Some subjects have missing values for certain behavioural regressors. Since I know there can't be empty cells in a FSGD (and thus in the design matrix), is it correct that my options are limited to either dropping the subject or filling in the missing cells with some "expected value", e.g. the mean value of that variable for the rest of the sample? > > 2) It says here that "NregressorsDOSS = Nclasses + Nvariables", which suggests you need regressors for group memberships, although such regressors are not present in any of the example FSGDs (and I've not included them in my file) > > 3) Because there are no membership regressors, and also because the "time dimension" (in my case: PRE or POST) is missing from this FSGD file, I am not sure how the contrast vectors should be built, given the longitudinal aspect of the data. So the research questions that I'd like these contrasts to ask are: > Where in the brain does thickness change significantly from PRE to POST, for the 3 different groups (pairwise)? > Where in the brain are these changes correlated with (each of) the behavioural measures? > For each subject, how is the change in thickness predicted by the PRE thickness value in that area, or by the behavioural regressors? In other words, can individual brain differences before training predict differences in learning abilities indexed after training? > Many thanks for your help! > Tudor > > > On 13 June 2014 17:27, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: > Hi Tudor, > > 1. There is a new version of freeview, I think you can download it somewhere. The tutorial also gives the tk surfer command line, which will work. But the visualization is not necessary. > 2.probably the qdec table has errors, eg different line breaks? Can you split it into blocks to see which block it does not load? > 3. To look at change you'd look at rate or percent change. Avg is just the average thickness of each subject across time. I never really used qdec, but probably you cannot do three groups. > > Best Martin > > > Sent via my smartphone, please excuse brevity. > > -------- Original message -------- > From: Tudor Popescu > Date:06/12/2014 10:00 PM (GMT+01:00) > To: free surfer > Subject: Re: [Freesurfer] Longitudinal design > > Hi Martin > > There were in fact some problems with the lGI values, as it wasn't clear at which of the 3 preprocessing steps (cross, base, long) the --pial_lgi flag had to be added. I asked about that in a different email, and meanwhile continued with the analysis for the existing measures (area and thickness). Issues I encountered: > > 1) After using the tutorial command > freeview -f subj/surf/lh.pial:overlay=subj/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=subj/surf/lh.long.thickness-stack.mgh:annot=subj/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale > I received errors about the option 'timecourse' and the sub-option flag 'annot_outline' being unrecongised. Is there a more recent version of freeview? I'm using FS 5.3, which I thought was the latest. Either way, I guess that this particular visualisation is not essential to the analysis. > > 2) When I load my cross.qdec.table.dat (attached) into QDEC, "Number of subjects" in the Subjects tab shows as 67, even though I have 72 subjects, all of which appear correctly entered on each line of the cross.qdec.table.dat ! > > 3) If I understood correctly, if one wants to see how thickness changed across time points and across the different groups, i.e. test the interaction, then "long.thickness-avg" has to be selected as Measure in QDEC. After doing this, and choosing group as a discrete factor, the mri_glmfit --y command fails with the errors "ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels". I guess this is because I have 3 groups and not 2. The question is, can I somehow do the 3 pairwise comparisons between my 3 groups in QDEC rather than at the command line (mri_glmfit) ? > > Many thanks! > Tudor > > > On 7 June 2014 23:24, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: > Hi Tudor. > For the mri_concat command at the end, does it work when you run it directly? It should not. Are the input files there. Is the dimension correct (you can run mri info on them). Since they are just surface maps, just like thickness, their dimensions should agree (eith each other and with thickness, and number of vertices of surfaces). > > Best Martin > > > Sent via my smartphone, please excuse brevity. > > > -------- Original message -------- > From: Tudor Popescu > Date:06/07/2014 9:55 PM (GMT+01:00) > To: Freesurfer support list > Subject: Re: [Freesurfer] Longitudinal design > > I should add that the commands for thickness, i.e. > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi ?h --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR > finished without error, and for some reason, so did the surface area commands, when I ran them a second time. > Also, I realised that for lGI, the flag for --meas was pial_lgi and not just lgi. However, the command > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas pial_lgi --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR > resulted in this error, similar for both hemispheres: > SUBJECT F02 Stacking Within-Subject Maps > mri_concat /vols/Scratch/tpopescu/learning/FS/F02_d1.long.F02/surf/rh.pial_lgi /vols/Scratch/tpopescu/learning/FS/F02_d5.long.F02/surf/rh.pial_lgi --o /vols/Scratch/tpopescu/learning/FS/F02/surf/rh.long.pial_lgi-stack.mgh > ERROR 1 : mri_concat stacking did not work? > > Thanks again for your help! > > > On 6 June 2014 17:45, Tudor Popescu <tudor3(a)gmail.com> wrote: > Hi Martin, thanks a lot for your answers. The slopes command is giving me errors though, see below. I also attach the long.qdec.table.dat that I'm using. I should point out that those ?h.long.cortex.label files mentioned in the error messages are in fact at their expected locations, and appear to be fine (i.e. are not size 0) > > In case anyone else can advice about question 1, I'd be really grateful! > > Command > Error > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas area --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR > > No such file or directory > mris_label_calc: could not open label file /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label > Invalid argument > mris_label_calc: mris_label_calc.cpp:127: int main(int, char**): Assertion `l2 != __null' failed. > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas area --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR > > mris_calc: could not open label file /vols/Scratch/tpopescu/learning/FS/F23/label/rh.long.cortex.label > Invalid argument > mris_calc: could not read label file /vols/Scratch/tpopescu/learning/FS/F23/label/rh.long.cortex.label > Invalid argument > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas lGI --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR > mris_label_calc: mris_label_calc.cpp:127: int main(int, char**): Assertion `l2 != __null' failed. > > SUBJECT F02 Intersecting Within-Subject Cortex Label > > cp /vols/Scratch/tpopescu/learning/FS/F02_d1.long.F02/label/lh.cortex.label /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label > > mris_label_calc intersect /vols/Scratch/tpopescu/learning/FS/F02_d5.long.F02/label/lh.cortex.label /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label /vols/Scratch/tpopescu/learning/FS/F02/label/lh.long.cortex.label > > ERROR -6 : mris_label_calc intersect did not work? > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas lGI --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time day --qcache fsaverage --sd $SUBJECTS_DIR > No such file or directory > mris_label_calc: could not open label file /vols/Scratch/tpopescu/learning/FS/F02/label/rh.long.cortex.label > Invalid argument > mris_label_calc: mris_label_calc.cpp:127: int main(int, char**): Assertion `l2 != __null' failed. > > > > > On 5 June 2014 16:00, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: > Hi Tudor, > > 1. not sure, this is a more general question for people more familiar with surfaces and edits > > 2. nothing is necessary, however, if you have regions where you find difficulties in some subjects, I'd look at that region in all subjects (e.g. you mention the posterior end). Usually if surfaces on the base are good, the long should be high quality also. > > 3. looks good (I'd do space separated, also some columns merged in your email and fsid-base for subject3 is wrong). > > 4. using the two-stage model you could do a pairwise analysis between your groups in the second stage, so linear mixed effects model is not necessary. In the two stage model, just think of it as a cross sectional analysis of e.g. thickness change, instead of thickness. > > 5. yes, is sutiable. You'd have to run it several times, once for each of the measures you want to analyze. You can drop some of: > > --do-avg --do-rate --do-pc1 --do-spc --do-stack > and only keep e.g. the rate or the pc1 (depending on what you want to analyze). You can also use --stack-rate to generate a stack of the rate maps. > > Best, Martin > > > On 06/04/2014 01:19 PM, Tudor Popescu wrote: >> Hi Martin, >> >> I reran everything from scratch and this time the recons ended without error. Few more questions: >> >> 1) Is the brainmask.mgz vs wm.mgz problem that I described in my previous email (surfaces only starting to show rather late at the posterior end of some subjects) something that I need to correct (e.g., by editing wm.mgz), or is it fine as it is? >> 2) Given that I visually inspected all bases, Is it necessary to inspect all slices for the longitudinal overlaps (vols+surfs) of all subjects, or is it enough to just check the central coronal slice for each subject? I ask because it's not just opening freeview with all those layers that is very slow, but also navigating between slices >> 3) The tutorial covers the creation of long.qdec.table.dat for a single-group scenario; I have 3 groups, with scans on the first and final (fifth) day of training, and was wondering whether the following table looks correct >> >> fsid fsid-base group day ageDemeaned >> gender score >> subj1_day1 subj1 treatmentA 1 1.34 f 109 >> subj1_day5 subj1 treatmentA 5 1.34 f 109 >> subj2_day1 subj2 treatmentB 1 -5.85 m 102 >> subj2_day5 subj2 treatmentB 5 -5.85 m 102 >> subj3_day1 subj2 control 1 3.06 f 98 >> subj3_day5 subj2 control 5 3.06 f 98 >> 4) Is this mixed design (3 groups and 2 time points, with both effect of group and of time being relevant) suitably analysed with only a simple 2 stage model, or is a linear mixed effects model necessary? Also, how are the stats different given there are 3 groups and not the usual 2 than most FS tutorials are based on? >> 5) Is the default long_mris_slopes command (which I understand does preliminary analyses, before going to QDEC) mentioned in the tutorial, i.e. >> long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR >> suitable for my particular case? I will also look at surface area and lGI, so I suspect it's at least "--meas area" and "--meas lGI" that I need to add to the above command? >> >> Thanks so much! >> Tudor >> >> >> >> On 3 June 2014 02:02, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: >> HI Tudor, >> >> you can run the -long processes in parallel. Something else is wrong. Check if you have enough disk space. Re-run the long from scratch (to make sure everything is generated new). >> >> Best, Martin >> >> On Jun 2, 2014, at 5:34 PM, Tudor Popescu <tudor3(a)gmail.com> wrote: >> >>> Hi Bruce >>> >>> I suspected this might be the case, since assessing 3D surfaces from a succession of 2D slices can be tricky, which is why I was wondering whether there's a better way to do these visual inspections. I checked those apparent artefacts in the other 2 planes (axial, saggital), but did not find it helpful in deciding whether the surfs was as they should or not. >>> >>> Something that I think is more likely to be a real problem (i.e., more than just a viewing plane disorientation), is that for many subjects, posterior slices only start to be followed by the surfaces quite late, e.g. from coronal slice 80 onward. This seems to be because those slices only appear in the brainmask.mgz, but not also in the wm.mgz (see screenshots attached). >>> >>> Also, after having run the cross and base steps, and ended up with folders of the type subj1_scanA, subj1_scanB etc, for the "long" step I launched simultaneously (for all subjects&scans) commands of the type >>> recon-all -long subj1_scanA subj1 -all >>> recon-all -long subj1_scanB subj1 -all >>> however these resulted in two types of error messages: >>> mghRead(/vols/Scratch/tpopescu/learning/FS/subj1_scanA.long.subj1/mri/aseg.mgz, -1): read error >>> (those particular aseg.mgz files had size 0kB), and >>> (standard_in) 2: Error: comparison in expression >>> I initially had disk space issues, but after making space I relaunched the same commands with the -no-isrunning flag, but with the same results. Is it the case that the long commands for the different scans of a subject have to be launched sequentially rather than in parallel, i.e. the command for scanB should be run after the command for scanA has finished? Otherwise, what could the problem be? >>> >>> Thanks again for your help. >>> >>> Tudor >>> >>> >>> >>> On 1 June 2014 15:17, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >>> Hi Tudor >>> >>> are you assessing the thickness visually? If so, you are probably being misled by the orientation of the surface w.r.t. the viewing plane. Same fo the apparent bubbles. You need to look in a different orientation >>> >>> cheers >>> Bruce >>> >>> >>> On Sun, 1 Jun 2014, Tudor Popescu wrote: >>> >>> Many thanks Martin and Nick! The rendering option was already checked, but >>> the freeview inspection commands were still very very slow, so I used >>> commands of the following form, which as far as I understand should be >>> equivalent: >>> tkmedit subjID norm.mgz -surfs >>> For several subjects (maybe 20 out of the total of 72), I noticed that the >>> surfaces don\t seem to quite follow the GM/WM demarcation line as expected - >>> for instance, by having portions of white surface (yellow line, see attached >>> screenshots) surrounded by pial surface (red line), or by having very large >>> cortical thickness in some parts of the brain. Is it possible that these >>> apparent artefacts make sense "in context" (by looking at the adjacent >>> slides), or is it the case that I need to go back and do white surface >>> correction, and then redo all 3 steps of the longitudinal process? >>> >>> Thanks again for your help! >>> Tudor >>> >>> >>> On 29 May 2014 17:39, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: >>> Tudor, >>> >>> in your virtual machine, make sure the 3D rendering option, or >>> 'use >>> hardware rendering' (or something like that) is enabled. this >>> would be on >>> the Windows VM config side of things. otherwise it will do >>> software >>> rendering which is painfully slow. >>> >>> Nick >>> >>> >>> > Hi Tudor, >>> > >>> > I don't think there is a way to speed things up. >>> > Let me know if you find a case where the template is blurry or >>> has >>> > ghosts. It should not happen, but if it does it indicates a >>> bad >>> > registratration, you'd have to run the mri_robust_template >>> command with >>> > different parameters manually then. >>> > >>> > Best, Martin >>> > >>> > On 05/27/2014 06:13 PM, Tudor Popescu wrote: >>> >> >>> >> Hi Martin, >>> >> Wasn't sure whether you'd seen my reply below, look forward >>> to hear >>> >> back your thoughts, thanks! >>> >> Tudor >>> >> >>> >> On 25 May 2014 21:40, "Tudor Popescu" <tudor3(a)gmail.com >>> >> <mailto:tudor3@gmail.com>> wrote: >>> >> >>> >> Thanks very much Martin and Bruce. I guess I'd misread the Wiki >>> >> (my own fault, not the text's), and am glad to hear that the >>> >> longitudinal pipeline is in fact perfectly suitable for my >>> needs >>> >> here. >>> >> >>> >> Having run the first 2 steps (cross and base), I'm a bit >>> unclear >>> >> how the output so far has to be manually inspected. It says in >>> the >>> >> tutorial >>> >> <http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial> >>> >> that you should load each subject's base volume + surfs in >>> >> freeview and then "move back and forth a few slices". However, >>> >> even just loading each base in this manner takes ~1 min on my >>> PC >>> >> (CoreDuo, 4GB, Ubuntu Virtualbox in Windows 7), and then moving >>> >> with PgUp/PgDn between all coronal slices (starting from the >>> >> default slice=128, going all the way posterior and then all the >>> >> way anterior) is excruciatingly slow. All of this would have to >>> be >>> >> repeated for all my 72 subjects - is there any way to optimise >>> >> this manual inspection? >>> >> >>> >> Also, if the surfs turn out to not follow the volume correctly, >>> >> presumably the thing to do is white surface correction + >>> >> re-running recon. But what should one do if, due to an >>> erroneous >>> >> averaging between timepoints, you see blurs/ghosts in your base >>> >> template? >>> >> >>> >> Many thanks! >>> >> Tudor >>> >> >>> >> >>> >> On 9 May 2014 21:33, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu >>> >> <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: >>> >> >>> >> Hi Tudor, >>> >> >>> >> the longitudinal pipeline in FS is actually one of the best >>> on >>> >> the planet as far as I know :-). If there is any >>> contradictory >>> >> information on the wiki, can you point me to that so I can >>> see >>> >> what causes the misconception. Really: compared to >>> independent >>> >> processing, it significantly increases sensitivity. Also we >>> >> have designed it to be unbiased with respect to a single >>> time >>> >> point or directionality. It is quite mature by now. >>> >> >>> >> You should definitely use the longitudinal pipeline for the >>> >> analysis of your data. Now to your questions >>> >> >>> >> 1. QDEC: I am not too familiar with qdec. You can >>> definitely >>> >> try the 2-stage approach described on the wiki. There you >>> >> first compute a measure of change (e.g. hippocampal volume >>> >> change during your week) and then compare that measure >>> across >>> >> groups similar to a cross sectional volume/thickness >>> analysis. >>> >> You can also use our tools to run a linear mixed effects >>> model >>> >> if you want to do that (it is more involved and requires >>> you >>> >> to use matlab tools). In your case, you probably have 2 >>> time >>> >> points for all subjects and the time distance is probably >>> the >>> >> same for all subjects, so the 2-stage approach should be >>> fine. >>> >> >>> >> 2. The image processing is done via the longitudinal >>> pipeline >>> >> (three steps: cross, base, long), to prepare the data look >>> at >>> >> the description of the 2-stage model >>> >> http://freesurfer.net/fswiki/LongitudinalTwoStageModel >>> >> and also the longitudinal tutorial >>> >> >>> http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial >>> >> >>> >> 3. At the recon all level in FS you get (after the 3 steps) >>> >> measurement for all time points. So you would compare those >>> >> results across time in the stats. >>> >> >>> >> Hope that helps, Martin >>> >> >>> >> >>> >> On 05/08/2014 08:14 AM, Tudor Popescu wrote: >>> >>> Sorry for the repeat, wasn't sure whether this was >>> received >>> >>> the first time. >>> >>> Tudor >>> >>> >>> >>> >>> >>> On 6 May 2014 19:55, Tudor Popescu <tudor3(a)gmail.com >>> >>> <mailto:tudor3@gmail.com>> wrote: >>> >>> >>> >>> Dear FS list, >>> >>> >>> >>> I have structural data from a learning study >>> >>> (pre&post-training scans, with 3 groups). Although the >>> >>> training was only one week, I'm guessing from an >>> analysis >>> >>> point of view, this still qualifies as longitudinal. I >>> >>> want to check for >>> >>> >>> >>> * the main within-subjects effect of time point >>> >>> (pre&post) >>> >>> * the main between-subjects effect of group >>> (treatment >>> >>> A, treatment B, control), >>> >>> * the time x group interaction >>> >>> >>> >>> I intend to look at thickness, surface area, volume, >>> and >>> >>> lGI. >>> >>> >>> >>> I read on the wiki >>> >>> >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing> >>> >>> that FS is currently not optimal for longitudinal >>> >>> analyses. I intend my FreeSurfer analysis to >>> supplement a >>> >>> VBM analysis done in FSL. In case it is in fact a good >>> >>> idea to do this, my questions (not covered in the >>> >>> 'longitudinal' wiki page) are: >>> >>> >>> >>> 1) Can QDEC be used for such an analysis, and if so, >>> what >>> >>> would be different as compared to a cross-sectional >>> (no >>> >>> temporal/within factor) study? >>> >>> >>> >>> 2) Also, is the pre-processing stage any different? >>> >>> >>> >>> 3) In FSL, for longitudinal designs you do stats on >>> >>> images obtained as the difference between consecutive >>> >>> time points. Does this have to be done in FreeSurfer >>> as >>> >>> well, and if so, is it done at the recon-all level or >>> >>> only at the stats (QDEC) level? >>> >>> >>> >>> Thanks! >>> >>> >>> >>> Tudor >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> >>> Freesurfer mailing list >>> >>> Freesurfer(a)nmr.mgh.harvard.edu >>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> >>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >>> >> -- >>> >> Martin Reuter, Ph.D. >>> >> >>> >> Instructor in Neurology >>> >> Harvard Medical School >>> >> Assistant in Neuroscience >>> >> Dept. of Radiology, Massachusetts General Hospital >>> >> Dept. of Neurology, Massachusetts General Hospital >>> >> Research Affiliate >>> >> Computer Science and Artificial Intelligence Lab, >>> >> Dept. of Electrical Engineering and Computer Science, >>> >> Massachusetts Institute of Technology >>> >> >>> >> A.A.Martinos Center for Biomedical Imaging >>> >> 149 Thirteenth Street, Suite 2301 >>> >> Charlestown, MA 02129 >>> >> >>> >> Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> >>> >> Email: >>> >> mreuter(a)nmr.mgh.harvard.edu >>> >> <mailto:mreuter@nmr.mgh.harvard.edu> >>> >> reuter(a)mit.edu <mailto:reuter@mit.edu> >>> >> Web :http://reuter.mit.edu >>> >> >>> >> >>> >> _______________________________________________ >>> >> 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. >>> >> >>> >> >>> >> >>> >> >>> >> _______________________________________________ >>> >> Freesurfer mailing list >>> >> Freesurfer(a)nmr.mgh.harvard.edu >>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> > -- >>> > Martin Reuter, Ph.D. >>> > >>> > Instructor in Neurology >>> > Harvard Medical School >>> > Assistant in Neuroscience >>> > Dept. of Radiology, Massachusetts General Hospital >>> > Dept. of Neurology, Massachusetts General Hospital >>> > Research Affiliate >>> > Computer Science and Artificial Intelligence Lab, >>> > Dept. of Electrical Engineering and Computer Science, >>> > Massachusetts Institute of Technology >>> > >>> > 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 >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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. >>> >>> >>> <02-06-2014, 22.17.45.png><02-06-2014, 22.17.55.png><only LH posterior.png><norm.png>_______________________________________________ >>> >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> --------------------------------- >> Dr. Martin Reuter >> 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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Martin Reuter, Ph.D. > > Instructor in Neurology > Harvard Medical School > Assistant in Neuroscience > Dept. of Radiology, Massachusetts General Hospital > Dept. of Neurology, Massachusetts General Hospital > Research Affiliate > Computer Science and Artificial Intelligence Lab, > Dept. of Electrical Engineering and Computer Science, > Massachusetts Institute of Technology > > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > > > > > <g3v9.fsgd> --------------------------------- Dr. Martin Reuter 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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Specify Brain Region as Dependent Variable
by Chris Wertz 24 Jun '14

24 Jun '14

Hi Freesurfer experts, Is it possible to change the dependent variable of a whole hemisphere's thickness to a specific brain region's thickness? For example I wish to test one of my independent variables with right hemisphere superior parietal region's thickness as opposed to the whole right hemisphere's thickness. Thanks, Chris

2 2

A comparison between atlases
by Dorian P. 24 Jun '14

24 Jun '14

Dear Freesurfer followers/developers, I am doing a study involving temporal lobes and the parcellations from Desikan and Destrieux atlases have very different results. I like the full gyrus parcellation of Desikan but the temporal pole is very small and limited, while in Destriux the temporal pole is bigger and more appropriate to be studied separately. My question is: can I combine parcellations from these atlases? I.e., if I subtract the temporal pole from Destriuex from the map of Desikan, will I take off all the anterior temporal pole gray matter, or is there any potential mismatch between parcellations so there will remain voxels in the anterior temporal lobe? Thank you. P.s. One less important question I have is this. I have noticed that wmparc.mgz is the same as aparc+aseg.mgz with the addition of white matter parcels. For Destrieux there is only the aparc.a2009s+aseg.mgz. Does this file have also the WM parcellation?

3 5

Extracting mean diffusivity values from diffusion data in freesurfer 5.3
by Rotem Saar 24 Jun '14

24 Jun '14

Dear freesurfer experts, I'm using freesurfer 5.3 for extracting FA and MD values for each region from the *aseg file for each subject. While I get validated FA values (I validated them with you, the literature and some other software I used), I have a problem getting reasonable MD values. This is the script I'm using for extracting the MD values: 1) dt_recon --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/I160.dcm --s Anatomy0981 --o /usr/local/freesurfer/subjects/Anatomy0981/DTI --b /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec 2) mri_label2vol --seg /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --temp /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --o /usr/local/freesurfer/subjects/Anatomy0981/DTI/forMD.mgz 3) mri_segstats --seg-erode 1 --seg /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/forMD.mgz --sum /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked It writes *.txt files similar to the ones of the FA (and also the volumetric analysis) which is good, but - 1) I can't understand the units (it is written "unknown"). can u tell me what do these units refer to ? 2) I can't understand why the units I get don't corresponds to the units in the literature (0-1). Is there a transformation I need to apply to these units in order to get the values we all see in the literature (MD values ranges between 0 to 1 in the papers I read). 3) I am concerned about the differences in the values both between and within subjects. For example, see 3 different subjects and their MD values for the corpus-callosum: subject 1: 35 251 368 368.0 CC_Posterior 7.4783 7.9938 0.0000 16.0000 16.0000 36 252 110 110.0 CC_Mid_Posterior 56.7273 476.3758 0.0000 5002.0000 5002.0000 37 253 205 205.0 CC_Central 992.4537 1806.8883 0.0000 5002.0000 5002.0000 38 254 132 132.0 CC_Mid_Anterior 1664.2954 2328.8467 43.0000 5002.0000 4959.0000 39 255 277 277.0 CC_Anterior 1723.4620 1914.7883 0.0000 5002.0000 5002.0000 subject 2: 36 251 328 328.0 CC_Posterior 0.0000 0.0000 0.0000 0.0000 0.0000 37 252 78 78.0 CC_Mid_Posterior 43.9744 226.6371 0.0000 2000.0000 2000.0000 38 253 100 100.0 CC_Central 203.0800 779.8602 0.0000 5001.0000 5001.0000 39 254 83 83.0 CC_Mid_Anterior 264.5783 364.1581 0.0000 1002.0000 1002.0000 40 255 321 321.0 CC_Anterior 985.8879 720.5300 0.0000 3028.0000 3028.0000 subject 3: 35 251 424 424.0 CC_Posterior 20.6840 6.6236 10.0000 60.0000 50.0000 36 252 160 160.0 CC_Mid_Posterior 143.4312 780.4187 0.0000 5001.0000 5001.0000 37 253 202 202.0 CC_Central 538.0248 1143.9441 0.0000 5001.0000 5001.0000 38 254 179 179.0 CC_Mid_Anterior 496.5140 623.4088 0.0000 2023.0000 2023.0000 39 255 361 361.0 CC_Anterior 211.6094 539.0007 0.0000 2028.0000 2028.0000 the values are really different both within the CC parts of the same subject (does this make any sense ??) and also between subjects... We ruled out a problem in the gradient matrix (both with you and because the FA values corresponds to reasonable values both from the literature and other software we use). Can u please advise on how can we solve this issue ? We are in the middle of submission of a very novel study and were required to show addition analysis of the MD values - this is why this is so impotent to us. Attached please find the full *.txt files I got. Thanks for your help. Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel

4 5

mri_ca_register error
by Liesel-Ann Meusel 24 Jun '14

24 Jun '14

Hi, I am running recon-all and I am getting the following error during the mri_ca_register step (full log file is attached). Please let me know what I need to do to fix it. Thank you, Liesel writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 4 hours, 17 minutes and 32 seconds. ERROR: mri_ca_register with non-zero status 1 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Sun Jun 1 22:03:47 EDT 2014 /home/lmeusel/101_TEST/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse ERROR: mri_ca_register with non-zero status 0 Linux gateway.neuroinfo.rri 2.6.32-279.9.1.el6.x86_64 #1 SMP Tue Sep 25 21:43:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 101_TEST exited with ERRORS at Sun Jun 1 22:04:52 EDT 2014 -- Liesel-Ann Meusel Postdoctoral Fellow Rm 722, Rotman Research Institute, Baycrest 3560 Bathurst St. Toronto ON M6A 2E1 416-785-2500 ext. 3507 lmeusel(a)research.baycrest.org

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