Freesurfer December 2011

freesurfer@nmr.mgh.harvard.edu

98 participants
157 discussions

Converting V1 labels to nifti
by Anders Hougaard 20 Dec '11

20 Dec '11

Dear Freesurfers, I would like to use V1 labels (created with the Hinds method) for a ROI-based analysis on data analyzed with FSL FEAT using FSL featquery. I have not run a full recon-all segmentation, only recon-all -s subjid -label-v1 I need to convert the labels to nifti volumes while registering to MNI standard space. I guess the right command would be something like mri_label2vol --label lh.v1.predict.label --reg register.dat --hemi lh --subject subject --o lh.v1.predict.label Is there a register.dat from the FSL feat directory that I could use for this? Anything else I need to add? Of course, I would like to keep the resulting volume probabilistic. All the best, Anders

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Opportunity for a research associate in MR imaging
by Direktion, Institut f. Schlaganfall- und Demenzforschung 20 Dec '11

20 Dec '11

The Hospital of the University of Munich, Germany, is one of the largest and most capable university hospitals in Germany and Europe. 45 specialized hospitals, departments and institutions harbouring excellent research and education provide patient care at the highest medical level with approximately 10.000 employees. The Institute for Stroke and Dementia Research (ISD) is a newly founded institution financed from foundation funds. The activity ranges from basic research to clinical trials (www.isd-muc.de) After completion of the construction phase, the Institute for Stroke and Dementia research will employ, around 100 staff members, graduate students, scholars and foreign scholars. The Institute for Stroke and Dementia Research (ISD) is looking at the earliest opportunity for a Research Associate in MR imaging RESPONSIBILITIES: We are looking for a motivated scientist with methodological expertise in MR imaging and good programming skills (e.g. C, C ++, Pearl, Python, Scripting Languages, Matlab). Knowledge in the collection, processing and analysis of functional and structural MR imaging data and an interest in neuro-scientific questions are desired. REQUIREMENTS: University degree. OFFER: Our Institute offers an excellent multidisciplinary environment (medical scientists, neuro-psychologists, biologists, bioinformaticians, epidemiologists) with modern IT infrastructure and defined times on human MR scanners (1.5T and 3T). A new building with its own small-animal-imaging (micro-PET and -MRI) is currently being built (www.isd-muc.de) The tasks include the establishment of new analytical methods for MRI-data, participation in ongoing research projects and developing of own project ideas. Salary is according to TV-L. The position is limited for two years, extension is desired. Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can unfortunately not be refunded. For more information, please contact Mr. Frühauf, Tel.: +49 (0)89 7095 7800 (E-Mail: isd(a)med.uni-muenchen.de) HOW TO APPLY: Your application - preferably in electronic form - with the usual documents indicating the earliest possible starting date should be directed to: Klinikum der Universität München, Institute for Stroke and Dementia Research Markus A. Frühauf, Managing Director ISD Heiglhofstr. 55 81377 Munich | Germany E-Mail: isd(a)med.uni-muenchen.de

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Use bbregister parameters to transform to EPI geometry
by Michael Waskom 20 Dec '11

20 Dec '11

Hi Doug, Is it possible to use the bbregister parameters to resample a functional image such that it is in register with the anatomical image but retains the epi geometry? I actually don't care so much about the epi-anat registration, but what I would like to be able to do is motion correct and otherwise preprocess my timeserieses within session* and then move different sessions into a common volumetric space for analysis. As I have great faith in bbregister, ideally the transformation would be determined with this method (I suspect it is superior to picking a slice from one of the sessions to use as a motion correction target across all sessions). Additionally, I would prefer not to upsample the source voxels either into 1x1x1 anatomical geometry or to surface vertices. Unfortunately, my affine understanding isn't deep enough for me to figure this out myself. Does that make sense, and (if so) do you have any ideas? Thanks! Michael * Here i use "session" in the sense of "run", which is different I think from FSFast terminology so apologies for any confusion.

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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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Freesurfer December 2011