Freesurfer

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19 participants
30088 discussions

Using subject-specific surface label as seeds on functional connectivity
by konglq＠nmr.mgh.harvard.edu 19 Dec '11

19 Dec '11

Hi Freesurfers, We are trying to do a resting-state functional connectivity analysis using freesurfer. Instead of using the aparc+aseg segmentations as seeds, we would like to use a subject-specific surface label that we have defined a priori as the seed region. In the fcseed-config step, what should we specify as the -segid and -seg (segmentation)? We have also looked into the ROI-based options but funcroi-config requires that we specify a contrast and an analysis which is not applicable here since we have already got our desired surface labels. Any help or suggestions are appreciated. Lingqiang

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FsFast Functional Connectivity
by Maya Rosen 19 Dec '11

19 Dec '11

Hi all, We've been trying to use FsFast for functional connectivity analysis using the left hippocampus as the seed (isolated from aseg). We used the following command to make the analysis: mkanalysis-sess -fwhm 0 -fsd bold -mcextreg -polyfit 2 -TR 2.6 -analysis lhippo_fcfsfast-analysis -nuisreg wm.dat 3 -nuisreg vcsf.dat 3 -nuisreg global.waveform.dat 1 -taskreg l_hippo.dat 1 -notask -native Note that we specified -notask. This ran fine. We then tried to run selxavg3-sess using this command: selxavg3-sess -s . -a lhippo_fcfsfast-analysis/ -no-preproc -no-con-ok and get this error: ERROR: not enough columns /r2/users/fspace2/RestData/091208RU_MR/bold/020/wm.dat ans = 116 1 This file has one column. And I assume that it is looking for multiple columns with which to do contrasts. However, this is resting-state data so there are no contrasts. Looking deeper into the selxavg3-sess code it seems that the -no-con-ok flag sets RequireContrast to 0. However, this does not get transferred to fast_selxavg3.m. DoContrasts = 1 in fast_selxavg.m. I think this is the problem. Any help would be greatly appreciated!!! Maya

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Re: [Freesurfer] bedpost failure using tracula
by Scott Hayes 19 Dec '11

19 Dec '11

Hi, The following files & directories are listed directly under dmri.bedpostX: bvals commands.txt logs nodif_brain_mask.nii.gz bvecs diff_slices monitor xfms --Scott Anastasia Yendiki Fri, 16 Dec 2011 09:43:47 -0800 Hi Scott - Are there any files created directly under dmri.bedpostX? a.y On Fri, 16 Dec 2011, Scott Hayes wrote: > 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Unpacking Error
by dmiller3＠bu.edu 19 Dec '11

19 Dec '11

Hello, I was hoping someone may know the answer to this. I am using freesurfer version 5.1. Using this command unpacksdcmdir -src DICOMS/"$1"_dicom -targ $1 -fsfast -scanonly $1/scan_"$1".txt where scan_name.txt lists the scan names used in the protocol and $1 is the subject's ID. I keep getting this error for my diffusion images: --------------------------------------------------------- Run 9 ----------------------------------------- Thu Dec 15 08:23:55 EST 2011 9 ep2d_diff_mddw_20_p2-MOD MGZ 009.mgz INFO: this run has an error, but trying anyway Files In Run: --------------- 04945195 ----------------------------- ERROR: reading DICOMS/TBI_B41_dicom//04945195 tag 28 30 I have two different sets of protocols and this is only happening for subjects with this protocol- exactly the same error with the same dicom (TENSOR dicom). However, when using another protocol I do not receive this error- and I have two different sets of scan names for them respectively. Any idea what this can be and how to fix- or if this will seriously affect processing if I just went on to manually convert the dti image? Thanks, Danielle Ph.D. Program in Behavioral Neuroscience Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 VA Boston Healthcare System Jamaica Plain Memory Disorders Research Center 150 South Huntington Ave D11-111 Boston, MA 02130 OFFICE:(857) 364-2853

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recon-all problems
by LAOUCHEDI MAKHLOUF 19 Dec '11

19 Dec '11

hi eveyone i ru the command recon-all of the 5.1 version of freesurfer on some subjects using the following arguments : recon-all -i database/ctr/ctr1 -subjid ctr1. it created a directory ctr1 in my SUBJECTS_DIR directory with all the sub-directories inside, but with no orig.mgz inside the mri sub-directory; instead of this, i found an empty directory named orig inside the directory named mri. the reconstruction ended with the following message : ERROR: no run data found in /home/mlaouche/freesurf_makh/ctr1/mri. Make sure to have a volume called 001.mgz in /home/mlaouche/freesurf_makh/ctr1/mri/orig. If you have a second run of data call it 002.mgz, etc. thanks

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turning off freeview "feature"
by Thomas Yeo 18 Dec '11

18 Dec '11

Hi, I noticed that when viewing multiple volumes in freeview (5.1.0, snow leopard), double-clicking on a volume will bring the volume to the top of the list of volumes. While this might be considered a feature, I am finding that when I am toggling a single volume on and off to visualize differences across volumes, a slight shift of the mouse will result in freeview interpreting this as a double click, causing the volume in question to pop up at the top of the list and I have to use the arrow keys to bring the volume back to the desired position. Is there any way I can turn the feature off? Thanks, Thomas

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Reliability and accuracy of Freesurfer
by MCLAREN, Donald 17 Dec '11

17 Dec '11

I've looked through a number of freesurfer papers, but haven't been able to find the answer to what I am looking for and was hoping someone had the references easily available. (1) What is the reliability of regional volumes generated from freesurfer over time? (2) What is the accuracy of labels for these volumes from subject to subject (e.g. how close are the freesurfer labels to cytoarchitecture or manually drawing the labels)? Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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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

1 0

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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