Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Recent error in the dev version
by Liu, Daniel 27 Jul '16

27 Jul '16

Hi, I'm an undergraduate learning about/working with freesurfer as part of my summer research project. In early-mid June I downloaded the dev version of Freesurfer to use on my mac. When I ran it at that time, I had no problem. Recently I started working on a cluster computer (linux) and got the same problem outlined in this exchange: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48412.html.<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48412.html> I was wondering if I could get an update on this and possibly an explanation as to what the problem was. I was told that the dev version on the cluster was updated today (with the fixed version as mentioned in the email) but I still got that message after running the program. Also, were there any major changes to the program that I should be aware about in terms affecting data analysis of the MRI patient data for the hippocampus subfields tool? If you could let me know, it would be appreciated. Thanks, Daniel

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Question about error
by Dorsa Haji Ghaffari 27 Jul '16

27 Jul '16

Hi, I ran recon-all on a series of dicom MRIs but it exited with errors, I have attached the recon-all.log here . I appreciate any suggestions. thank you Dorsa

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TRACULA: 20% default threshold
by Newbold, Dillan 27 Jul '16

27 Jul '16

Hi everyone, I’m having a little trouble understanding the exact meaning of the 20% default threshold used in the freeview -tv option and dmri_pathstats --pthr. I’ve seen multiple threads where Anastasia said that it is 20% of the maximum value in the probability distribution—which corresponds to the maximum number of sample paths intersecting a single voxel—but the default thresholds I’ve seen set by the -tv option are generally lower than that. For example, I have one subject in whom the right CST has a maximum value in its path.pd.nii.gz file of 300. I would expect based on what I’ve read in the mail archives that the threshold would be set at 60, but when I open the merged file with the -tv option the default threshold for the right CST is 35. My current best guess is that the default threshold is set to produce a volume that has a probability sum equal to 20% of the sum of the pre-threshold volume. (That is, the sum of intensities of all voxels in the path.pd.nii.gz file should be 5 times the sum of the voxels above the default threshold.) Is that accurate? Thanks for all you’ve done to develop this tool. It’s brilliant and I want to understand as much of it as I can. -Dillan

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TRACULA fornix tractography
by Barbara Kreilkamp 27 Jul '16

27 Jul '16

Dear Anastasia, As we are analyzing DTI data acquired in patients with epilepsy we are especially interested in the fornix. I've come across the mri_cc -f option for fornix segmentation (native space) but I've also read that manual tracing/labeling of the tracts would be needed in the 33 controls for TRACULA (training set - trctrain). In Wakana et al. 2011 I see that the fornix was not included due to low reproducibility and it further states: "the reason for the poor reproducibility is most likely due to not enough spatial resolution with respect to the diameter" I wonder if you could please guide us in how to best add this tract to TRACULA so that it would be consistent in the methods compared with the other tract ROI definitions or perhaps state what were the difficulties in adding this particular tract to TRACULA. Thank you very much, Best wishes, Barbara

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problems by running longitudinal mass univariate analysis
by Valsasina Paola 27 Jul '16

27 Jul '16

Dear FS experts I am trying to run the commands for performing the longitudinal mixed effect statistics with the LME Matlab toolbox. I am following the instructions on the web page; however, I have two questions: 1) when I run the command lme_mass_fit_vw, the script is running for a very long time, after 3 hours the estimation was just at 10% (unfortunately, my laptop is equipped with Windows and is not particularly powerful). I had to stop the script at that point; before restarting it again I would like to be sure: is this behavior normal? Is it correct that lme_mass_fit_vw is running for such a long time? 2) when the script was running, there were several warnings on the Matlab screen, saying that the algorithm was not converging (at most of locations). Is it also normal? How can I check the correctness of my input image? When I open with freeview the "lh.thickness_sm10.mgh" volume, I just see a black screen with valid timeseries values in the minority of voxels (I imagine that these timeseries are concatenated thickness values of my study subjects). Is there another way to better visualize and check a concatenated 4d mgh file? Failure of convergence is referring to empty/zero voxels of this image? Thank you for any advice on these two topics Kind regards Paola Rispetta l'ambiente: non stampare questa mail se non ? necessario. Respect the environment: if it's not necessary, don't print this mail. IL TUO 5XMILLE AL SAN RAFFAELE DI MILANO Devolvi il tuo 5 per mille all'Ospedale San Raffaele: perch? al centro della Ricerca ci sei TU. CODICE FISCALE: 07636600962, nel riquadro RICERCA SANITARIA. Non c'? cura, senza ricerca. Non c'? ricerca, senza il tuo 5xmille. Scopri come su http://www.5xmille.org [http://www.5xmille.org/img/731x129.jpg]

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Error with selxavg3-sess
by Luft, Marissa 27 Jul '16

27 Jul '16

I am running the following code: selxavg3-sess -s 1002a -analysis workmen.sm05.lh on data that was already preprocessed with preprocesses, mkanalysis-sess, and mkcontrast-sess. I get the following error message: outanadir = /Users/marissaluft/Documents/ROSE_Program/Jeff_Lab/Free_Surfer_Project/Project_Folder/1002a/bold/workmem.sm05.lh Subscripted assignment dimension mismatch. Error in fast_ldpar4 (line 97) par4(nthrow,1) = tonset; Error in flac_customize (line 121) [par partype] = fast_ldpar4(parpath); Error in fast_selxavg3 (line 115) flac = flac_customize(flac); Thank you, Marissa Luft

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TRACULA dmri_paths, single time point in longitudinal stream
by Harms, Michael 27 Jul '16

27 Jul '16

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doubts about pial surface
by Elias Vergílio Da Cás 27 Jul '16

27 Jul '16

Hi, My name is Silvia and I would like to know how to edit the pial surface conform image in the attachment. I've tried painting with grey color but it wasn't successful and when I erase the voxels around the region nothing happens too. *Freesurfer version*: 5.3 -- Atte. Elias Vergílio Da Cás - Físico UFES/HUCAM/EBSERH

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flipping TRACULA tracts
by Barbara Kreilkamp 27 Jul '16

27 Jul '16

Dear Freesurfers, I've got data pertaining to patients with left and right-sided temporal lobe epilepsy (TLE). My aim is to group those tracts according to side of epilepsy for waypoint comparisons. Basically for patients with right TLE I'd like to look at right tracts and at the same time for patients with left TLE I'd like to look at left tracts (ipsilateral tracts), I need to do the same for the contralateral tracts. Is there a straightforward way of doing this? I've already copied the tracts to respective ipsi and contralateral byvoxel.txt files. Like so: for i in R*/dpath/rh*/pathstats.byvoxel.txt; do cp $i ${i/byvoxel./byvoxel_ipsiRTLE.}; done ; for i in R*/dpath/lh*/pathstats.byvoxel.txt; do cp $i ${i/byvoxel./byvoxel_contraRTLE.}; done Now I have to flip the x-coordinates in the patients with right TLE (to make them more comparable to the tracts of the patients with left TLE). That will not be a problem, but I wonder if I am missing something? Can I then just go ahead and run trac-all -stats -c dmrircfile to generate the mean waypoint tracts etc.? Thank you very much, Best wishes, Barbara

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TRACULA group stats visualization
by Derek Pisner 27 Jul '16

27 Jul '16

Dear Anastasia, I am running into an issue with the trac-all -stat option on our longitudinal TRACULA data. Everything runs smoothly through all earlier stages, and I checked individual subjects' merged outputs in freeview with -tv mode. Everything looks fine. Also, then when I run trac-all -c dmric_config -stat, everything finishes without error. But then when I open the results with the command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt I get the image seen in the attached .png file. Any idea what might be causing this? Many thanks in advance for you help. Best, Derek

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