Freesurfer December 2011

freesurfer@nmr.mgh.harvard.edu

98 participants
157 discussions

Re: [Freesurfer] Tracula wiki updates & work-around suggestions
by Priti Srinivasan 16 Dec '11

16 Dec '11

Hi Shannon, Thank you for the detailed email, outlining some of the aspects of the tutorial that we could improve. We really appreciate your effort in putting these things together and will definitely try to address your concerns to the best of our ability. Q2. I updated the wiki to correct the typo with the configuration file. It was an oversight on my part. Q4. The Tractography output section (and in general all steps in the tutorial) is targeted keeping in mind, the tracula tutorial data that is available for download. Here we've used one of the training subjects for as an example subject and hence we used only the remaining 32 subjects for training. If you were to use your own data (and not the tutorial data downloaded from the freesurfer website) you would be using all 33 training subjects and hence it should be updated to merged_avg33_mni_flt.mgz (As you're using all 33 subjects for training). I can add a little note in the wiki for people processing their own data about the output file names they should expect. Thanks, Priti > Hi Tracula team, > > > > I have just successfully processed my first scan through > all > the Tracula steps! Though, I have to say it could have gone much smoother > / > quicker if the documentation on the wiki were a little more up-to-date. I > realize it's an ongoing struggle to keep documentation current, so I > thought > I'd send you my observations as I worked through all the bumps in the > road. > You are probably aware of most of these issues but here they are in one > big > email for you to consider: > > > > 1. I'm unable to find anything among the Tracula setup instructions > where it says which version of FSL that Tracula requires, and this version > issue was a crucial piece of the puzzle. I had been failing at step 2 with > an older version of FSL (v4.1.4), and per your suggestion I updated to > v4.1.9. However, when called by Trac-all -bedp, bedpostx ALWAYS failed to > created the "merged*.nii.gz" files for me, even after modifying it and > updating FSL versions. I'm not sure why that is but it may be helpful to > users to know they can simply bypass that step by launching bedpostx > separately in the latest FSL, and pointing it at the "dmri" folder created > during the Trac-all -prep stage. Also, we had to modify "bedpostx", as > well > as "fsl_sub", to get it to launch to our cluster without issues. Once all > the fixes were in place, this step took only an hour or two to run. I then > copied bedpostx's outputs into the requisite "dmri.bedpostX" directory to > launch the -path step, and it completed in about an hour. Launching > "bedpostx_datacheck <dmri folder>" beforehand was very helpful for > troubleshooting the prep stage. > > 2. There is a typo in the description of the configuration file > setup: > "set dorotvecs" is listed in the detailed description under Step9, but > this > is incorrect and will cause errors. It's a bit confusing because it is > correctly listed as "set dorotbvecs" in the complete config file example > you > provide above that section. It's unclear which one is correct and forces > users to debug something which they probably have never run before. > > 3. Also in the config file is the variable $FSLDIR, which I > discovered > we had to set after receiving errors during mni registration. I suppose > the > setting of that variable should be obvious, but it wasn't clear based on > the > example which folder, exactly, should be associated with that variable > name. > We set our $FSLDIR to the /bin folder and all was well. Entirely possible > this is just a lab-specific issue on our end. Since this variable needs > to > be set properly, just like the $SUBJECTS_DIR, perhaps this information > could > be included towards the top of the page where the rest of the required > environmental variables are mentioned? > > 4. Finally, in the "Tractography Outputs" section, the command line > example given needs to be updated because it shows > "lh.ilf_AS_avg32_mni_flt" > as example. The "32" should be "33". The same goes for > "merged_avg32_mni_flt.mgz", obviously. > > > > Until very recently, I was experiencing all the same issues Scott Hayes > has > been reporting lately. (The singular "Data_slice_0002" folder, with > missing > files, and the over-and-over messages of "1 slices processed" in a > terminal > that never throws an error message despite its failure. During the > subsequent -path step, without those "merged*.nii.gz" files, I would > receive > the dreaded & perplexing "Word Too Long" error. A more specific error > message regarding the missing files might be more useful for > troubleshooting > purposes.) > > > > Many thanks for all your advice and help throughout the process! We can > now > move forward and do some exploration... Very exciting! > > > > Shannon T. Buckley > SRA III - Supervisor > CIND, UCSF > 4150 Clement St. (114M) > San Francisco, CA 94121 > Phone: (415) 221-4810 x4251 > Fax: (415) 386-3954 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Tracula wiki updates & work-around suggestions
by Shannon Buckley 16 Dec '11

16 Dec '11

Hi Tracula team, I have just successfully processed my first scan through all the Tracula steps! Though, I have to say it could have gone much smoother / quicker if the documentation on the wiki were a little more up-to-date. I realize it's an ongoing struggle to keep documentation current, so I thought I'd send you my observations as I worked through all the bumps in the road. You are probably aware of most of these issues but here they are in one big email for you to consider: 1. I'm unable to find anything among the Tracula setup instructions where it says which version of FSL that Tracula requires, and this version issue was a crucial piece of the puzzle. I had been failing at step 2 with an older version of FSL (v4.1.4), and per your suggestion I updated to v4.1.9. However, when called by Trac-all -bedp, bedpostx ALWAYS failed to created the "merged*.nii.gz" files for me, even after modifying it and updating FSL versions. I'm not sure why that is but it may be helpful to users to know they can simply bypass that step by launching bedpostx separately in the latest FSL, and pointing it at the "dmri" folder created during the Trac-all -prep stage. Also, we had to modify "bedpostx", as well as "fsl_sub", to get it to launch to our cluster without issues. Once all the fixes were in place, this step took only an hour or two to run. I then copied bedpostx's outputs into the requisite "dmri.bedpostX" directory to launch the -path step, and it completed in about an hour. Launching "bedpostx_datacheck <dmri folder>" beforehand was very helpful for troubleshooting the prep stage. 2. There is a typo in the description of the configuration file setup: "set dorotvecs" is listed in the detailed description under Step9, but this is incorrect and will cause errors. It's a bit confusing because it is correctly listed as "set dorotbvecs" in the complete config file example you provide above that section. It's unclear which one is correct and forces users to debug something which they probably have never run before. 3. Also in the config file is the variable $FSLDIR, which I discovered we had to set after receiving errors during mni registration. I suppose the setting of that variable should be obvious, but it wasn't clear based on the example which folder, exactly, should be associated with that variable name. We set our $FSLDIR to the /bin folder and all was well. Entirely possible this is just a lab-specific issue on our end. Since this variable needs to be set properly, just like the $SUBJECTS_DIR, perhaps this information could be included towards the top of the page where the rest of the required environmental variables are mentioned? 4. Finally, in the "Tractography Outputs" section, the command line example given needs to be updated because it shows "lh.ilf_AS_avg32_mni_flt" as example. The "32" should be "33". The same goes for "merged_avg32_mni_flt.mgz", obviously. Until very recently, I was experiencing all the same issues Scott Hayes has been reporting lately. (The singular "Data_slice_0002" folder, with missing files, and the over-and-over messages of "1 slices processed" in a terminal that never throws an error message despite its failure. During the subsequent -path step, without those "merged*.nii.gz" files, I would receive the dreaded & perplexing "Word Too Long" error. A more specific error message regarding the missing files might be more useful for troubleshooting purposes.) Many thanks for all your advice and help throughout the process! We can now move forward and do some exploration... Very exciting! Shannon T. Buckley SRA III - Supervisor CIND, UCSF 4150 Clement St. (114M) San Francisco, CA 94121 Phone: (415) 221-4810 x4251 Fax: (415) 386-3954

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bedpost failure using tracula
by Scott Hayes 16 Dec '11

16 Dec '11

Hi, After I run step 2 of tracula (>trac-all -c config_DTI_B.txt -bedp), I am missing multiple bedpost output files (e.g., mergedph1samples.nii). Examining the output, it looks like data from only one slice was written (dmri.bedpostX/diff_slices/data_slice_0002). This issue has replicated across multiple subjects. I'm processing data locally on mac os 10.6.8 (16 GB RAM; two 3.2 quadcore processors, which should be able to handle bedpost), using FSL 4.1.9. I don't see any errors in the tracula log files (until I run -path), and no complaints in the terminal window (which writes: Queuing parallel processing stage 0 slices processed 1 slices processed 1 slices processed etc... Any insight as to what might be causing the issue? Thanks, Scott

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mri_cc and CC thickness option...
by Gonzalo Rojas Costa 16 Dec '11

16 Dec '11

Hi: For example, if I execute the mri_cc command with "-t 2", mri_cc shows me "setting callosum thickness to 5 mm"... Why ?... What exactly specify the -t option ?... Sincerely, Gonzalo Rojas Costa

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run preproc-sess with -nomc
by Thunell Evelina 16 Dec '11

16 Dec '11

Hi, Does anyone know how to correctly use the -nomc and -noreg flags? When I run: preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc I get the error message: ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr I also tried preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg which gives the error: ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat Try running register-sess with -per-run When I do preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold it works fine and finishes without errors (preproc-sess done) (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8) Thanks a lot for any help, Evelina

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Estimate Brain Volume Fraction
by Cheryl McCreary 15 Dec '11

15 Dec '11

Hi Freesurfer experts, I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct? I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available. My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well? Thanks for your help. Cheryl -- Cheryl McCreary Seaman Family MR Research Centre Foothills Medical Centre 1403 29th Street NW Calgary, AB T2N 2T9

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ICV and regional brain volumes
by Lugar, Heather 15 Dec '11

15 Dec '11

We are having a difficult time getting the ICV to fit correctly in our sample, but the segmentions and parcellations look accurate. I believe that the ICV is generated from the talairach.xfm early on in the processing stream, but then further processing for segmentations/parcellations is done. So, does the ICV measure affect regional brain volumes in any way, or can we trust the volumetric measures to be accurate even if the ICV is not? Thank you, Heather Lugar

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(no subject)
by Adam Nitenson 15 Dec '11

15 Dec '11

Hi Doug et al, We have been working on a linear regression-type analysis (see attached analysis.info for analysis and slopepar for a sample paradigm file) that involves task-related activation in a working memory test. For each participant, there are four conditions: 1, 3, 5, and 7 items that need to be remembered. The question that we would like to ask is: for each voxel, does the slope of activation (i.e., the slope of the best-fit line as you move from 1 to 3 to 5 to 7 items, as calculated separately for each subject) differ from zero? The second-level analysis would determine if there is a significant difference in activation-related slope between groups. Based on previous discussion, the way we have been doing this is to modify the paradigm file to create the following contrast: Condition 2: activation during working memory, but weighted by condition so the 1 item condition is weighted as 1, the 3 item condition as 3, etc. Condition 0: fixation The contrast is Condition 2 minus Condition 0. However, this method of weighting does not appear to answer the question about slope, but rather focuses on a weighted average. Consider the following scenario, involving 5 subjects (A through E): The SLOPE column is calculated using the slope function of the spreadsheet (i.e., slope of best fit line, using values of 1...3...5...7 for the x-axis, and, say, for subject A, the values of 2...4...6...8 for the y-axis). The WEIGHTED column is calculated in the way that I think FS-FAST is doing it, which is as follows: ((1 * 1 item activ. value) + (3 * 3 item activ. value) + (5 * 5 item activ. value) + (7 * 7 item activ. value))/4 The SLOPE and WEIGHTED values (regardless of their different scale) are not really comparable. For example, for Subject A, the SLOPE value is 1 and the WEIGHTED value is 58, while for Subject E, the SLOPE value is 1.1 and the WEIGHTED value is 28. So when looking at the paradigm file, take the lines 76.57 2 3.4 5 213.42 2 2.29 7 Does this mean that the activation at the first timepoint is accounted for 5-fold and the second timepoint 7-fold? If this is the case then this analysis may not best represent what we are looking for. Is there a way to modify the paradigm file so that the analysis can focus on slope of the best fit line as opposed to the weighted average? Thanks, Josh Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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Re: [Freesurfer] Freesurfer Digest, Vol 94, Issue 13
by Maryam Vaziri Pashkam 15 Dec '11

15 Dec '11

Hi, Following up on the preprocessing error: > Can't connect? tcp_connect[connect]: Connection timed out We figured where the problem is. This error came out when freesurfer calls an afni function. Apparently it tries to check which version of afni it is using against the internet to find out the most recent version. Suppressing the afni version check solved the problem. I just added this line to my .bashrc file: export AFNI_VERSION_CHECK=NO Maryam On Mon, Dec 12, 2011 at 12:00 PM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. preprocessing error (Maryam Vaziri Pashkam) > 2. Re: preprocessing error (Douglas Greve) > 3. convert surface label on to functional image (Zhangyuanchao) > 4. References/materials for interaction analysis in freesurfer > (Bhavani Shankara Bagepally) > 5. Re: dt_recon error (Yuko Yotsumoto) > 6. Re: dt_recon error (Yuko Yotsumoto) > 7. Re: run preproc-sess with -nomc (Thunell Evelina) > 8. Re: mri_ca_register from virtual box (Lorenzo Busti) > 9. Re: mri_ca_register from virtual box (Lorenzo Busti) > 10. Converting thickness maps to vtk (Navid Shiee) > 11. Re: tracula and snow leopard: can't allocate region / memory > error (Anastasia Yendiki) > 12. tracula failed to find header file for -t (Scott Hayes) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 11 Dec 2011 14:34:05 -0500 > From: Maryam Vaziri Pashkam <mvaziri.p(a)gmail.com> > Subject: [Freesurfer] preprocessing error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAEEXA4cePaYDO8EPMpma7ThADfnd1qcYfg2HnnHz+7sVrVBTjw(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I am running preprocessing on my data using freesurfer 5.1, fsl 4.1.7, and > matlab R2009a (I also tried it with matlab 2007a) on Harvard cluster and I > am receiving an error. I connect to the cluster using terminal and SSH > connection in mac. > > the preprocessing is stalled in the middle with this error: > > ++ Max displacement in automask = 0.79 (mm) at sub-brick 3 > Can't connect? tcp_connect[connect]: Connection timed out > ++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz > ** Warning: overwriting file 004/fmcpr.mcdat > Can't connect? tcp_connect[connect]: Connection timed out > Can't connect? tcp_connect[connect]: Connection timed out > Can't connect? tcp_connect[connect]: Connection timed out > > > It does not stop running and output an error. But rather keeps printing the > last line and does not move forward. Any idea where the problem might be? > > > Thanks, > Maryam >

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nWBV
by Lindsay Ercole 15 Dec '11

15 Dec '11

How might we obtain nWBV from the FS data? What variables could be summed or what variable could be used individually and adjusted to create a nWBV? Does total gray include cerebellar gray, but total white volume does not include cerebellar white? Sincerest thanks! Lindsay

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Freesurfer December 2011