Re: [Freesurfer] Tracula: missing or incomplete tracts
Hi Anastasia, Sorry for the delay -- I missed your response. I did look at the anatomical segmentations and thought they looked OK. I've uploaded the tracula and corresponding freesurfer data for two subjects: one with complete tracts and one with missing/incomplete tracts. I also uploaded my dmrirc file. Thanks for taking a look for me. Eileen. Hi Eileen - Have you checked the anatomical segmentations of the subjects? The mask that's used by default is the aparc+aseg_mask, which comes from registering the cortical parcellationg and subcortical segmentation from T1 to diffusion space, and then dilating it by a couple of voxels. If you upload an example data set for me here, I can take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Please include all tracula-related directories of the subject (dmri, dlabel, etc). Thanks! a.y On Thu, 18 Dec 2014, Eileen Moore wrote: Hi - I'm having difficulty with missing or incomplete tracts most of my subjects. I'm hoping for suggestions on where I can look for data problems. The majority of my subjects have at least one missing/incomplete tract, but the specific problematic tract varies across subjects (e.g., one subject has a missing L.Uncinate; another subject has a missing Forceps Major; another is missing the ILF bilaterally, etc.). For my problematic tracts, the path.pd.nii.gz is a single line/curve rather than the diffuse volumetric distribution. I'm not sure how to correct this. I have checked my eigenvectors -- the lines appear to be pointing in the correct directions in my dtifit_V1 -- so I believe my gradient table is correct I've checked my images for motion via visual inspection and by excluding any subjects with dwi_motion outliers in AvgTranslation, AvgRotation, PercentBadSlices, and AvgDropoutScore. I inspected the nodif_brain_mask.nii.gz to look for chunks of missing brain and did not identify any problems here. I've tried increasing the number of control points for each tract. I'd very much appreciate any suggestions on how to troubleshoot next. Thank you, Eileen. ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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@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] Generating individual statistics on a manually traced segmentation/label
Hello FreeSurfer experts, I am using freesurfer v5.3 on a linux os. I have a few questions regarding individual aseg statistics (volume, intensity) for a subcortical region that is not automatically segmented by freesurfer. Using tkmedit I have manually traced my subcortical ROI and saved it as a label. By looking at the label for each subject (i.e., less /label/ROI.label ) I can see how many voxels are included in the label, the coordinates of each voxel in the label and the signal intensity of each of these voxels. 1. Is there anyway to transform the information in my label to individual statistics in a format similar to what I can obtain with the automatic segmentations and asegstats2table? And what additional steps are necessary to accomplish this? 2. Does the volume that was loaded when the label was created have an impact on any of the volume statistics computed? For example, I generated my label on each subject with the orig volume loaded (i.e., tkmedit orig.mgz ) - if I label the same voxels on the norm.mgz, will the intensity values generated for each subject be different? And should I have used a different volume to create my labels? 3. In the label, what coordinate system is used to identify the labeled voxels? Are these coordinates in native space? Thanks, Eileen. Sent from my iPad ___ Freesurfer mailing list 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] San Diego NIAAA T32 Postdoc Opening
San Diego NIAAA T32 Postdoc Position Opening Announcement A postdoctoral position in alcohol research is available now through an NIAAA T32 institutional training grant between SDSU and UCSD in San Diego, CA. Postdoctoral appointees are supported for twelve-month, full-time appointments with the ability to receive up to two years of support based upon acceptable progress during their initial year. Qualified candidates must be U.S. citizens (or permanent resident or noncitizen national of the U.S.) and have completed their doctoral degree requirements in the clinical and behavioral sciences. Specific areas of alcohol research include fetal alcohol spectrum disorders, adolescent and adult alcohol/substance use disorders, risk and protective factors for alcoholism, alcohol and brain disease, neurobiological/behavioral effects of alcoholism, neuropsychological function, structural and functional neuroimaging, interventions, and psychiatric and medical comorbidity. Fellows will conduct research with their mentor, including comprehensive literature reviews and participation in data collection and analysis. Fellows are expected to become involved in manuscript and grant writing, to participate in alcohol research training program seminars, and present at national meetings (e.g., Research Society on Alcoholism). Faculty mentors include Drs. Edward Riley (Director), Susan Tapert (co-Director), Robert Anthenelli, Kara Bagot, Sandra A. Brown, Mariana Cherner, Cindy Ehlers, Jay Giedd, Igor Grant, Joanna Jacobus, Terry Jernigan, Ksenija Marinkovic, Sarah Mattson, David Moore, Mark Myers, Sonya Norman, Marc Schuckit, Andrea Spadoni, Michael Taylor, Jennifer Thomas, Ryan Trim, Tamara Wall, and Matt Worley. To apply please complete the online form (http://niaaa-t32.sdsu.edu/apply/) and submit your CV, personal statement, and the names of three references to Edward Riley's assistant, Jill Vander Velde, at vand...@mail.sdsu.edu. ___ Freesurfer mailing list 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.
Re: [Freesurfer] trac-all -prep error field map error
Hi Anastasia, OK - our imaging physicists had developed a wrapper script around epidewarp which takes our dicom images and converts them into the phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). It looks like the tracula script requires dicom images. Is there a way for me to do epidewarp manually and then follow through with the remaining steps using trac-all? Thanks, Eileen. Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > From: Anastasia Yendiki > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: Freesurfer support list > Message-ID: > Content-Type: text/plain; charset="utf-8" > > > Hi Eileen - That step is run with the program epidewarp.fsl, which you can > run on the command line to see the available options. The input phase map > volume is expected to have either 2 frames (2 separate phase maps) or 1 > frame (the difference phase map). This error from trac-all means that it > found that your input phase map has something other than 1 or 2 frames, so > it doesn't know how to handle it. > > Hope this helps, > a.y > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. I'm tyring > to > > run tracula on some? images acquired from a GE scanner. I am running into > > problems when I try to perform the registration-based B0-inhomogeneity > > compensation, getting an error in the terminal output: "ERROR: > Unrecognized > > format of phase map". However, trac-all -prep runs fine when I skip the > > B0-inhomogeneity compensation step. Is there something else I need to do > to > > use field map correction? > > > > I've attached the trac-all.log and a copy of the terminal output. > > > > Thanks, > > Eileen. > > > > > > > > > ___ Freesurfer mailing list 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.
Re: [Freesurfer] trac-all -prep error field map error
Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example? As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for the fBIRN consortium). In the tutorial dmrirc example I see only the 'set b0mlist' and 'set b0plist' options, and am unsure where I could give it the phase difference map. I've also tried converting the dicom magnitude and phase maps to nifti format and inputting these into the dmrirc file but I am still getting an error. (See attached log file). Thanks, Eileen. > -- > > Message: 10 > Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) > From: Anastasia Yendiki > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: Freesurfer support list > Message-ID: > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Eileen - All image formats that mri_convert (and thus any freesurfer > program) can read will do, you don't need dicom. Try giving trac-all the > phase difference maps you have and let's see what happens. > > Best, > a.y > > On Wed, 16 Jul 2014, Eileen Moore wrote: > > > Hi Anastasia, > > > > OK - our imaging physicists had developed a wrapper script around > epidewarp > > which takes our dicom images and converts them into the phase difference > map > > (it is based on the script that was authored by Doug Greve for the fBIRN > > consortium). It looks like the tracula script requires dicom images. Is > > there a way for me to do epidewarp manually and then follow through with > the > > remaining steps using trac-all? > > > > Thanks, > > Eileen. > > > > > > Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > > From: Anastasia Yendiki > > Subject: Re: [Freesurfer] trac-all -prep error field map error > > To: Freesurfer support list > > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > > > > > Hi Eileen - That step is run with the program epidewarp.fsl, > > which you can > > run on the command line to see the available options. The input > > phase map > > volume is expected to have either 2 frames (2 separate phase > > maps) or 1 > > frame (the difference phase map). This error from trac-all means > > that it > > found that your input phase map has something other than 1 or 2 > > frames, so > > it doesn't know how to handle it. > > > > Hope this helps, > > a.y > > > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. > > I'm tyring to > > > run tracula on some? images acquired from a GE scanner. I am > > running into > > > problems when I try to perform the registration-based > > B0-inhomogeneity > > > compensation, getting an error in the terminal output: "ERROR: > > Unrecognized > > > format of phase map". However, trac-all -prep runs fine when I > > skip the > > > B0-inhomogeneity compensation step. Is there something else I > > need to do to > > > use field map correction? > > > > > > I've attached the trac-all.log and a copy of the terminal > > output. > > > > > > Thanks, > > > Eileen. > > > > > > > > > > > > > > > > > > > > freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/image/FASD/Shared/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl brain:~> cd freesurfer/ brain:~/freesurfer> ls DICOM_FILES FreeSurfer_Scripts sessions subjects tracula brain:~/freesurfer> cd tracula brain:~/freesurfer/tracula> ls CIFASD2-DTI-pilot CIFASDII_T1-DTI dmrirc.example DTI-30 DTI-30_pilot error.log brain:~/freesurfer/tracula> cd CIFASDII_T1-DTI/ brain:~/freesurfer/tracula/CIFASDII_T1-DTI> ls bvals call1285_CIFASDII_T1_021210 dmrirc.CIFASDII_T1-DTI~ terminal-output-error.txt bvecs dmrirc.CIFASDII_T1-DTI dmrirc.file brain:~/freesurfer/tracula/CIFASDII_T1-DTI&
Re: [Freesurfer] trac-all -prep error field map error
Hi - I still have not been able to apply the field map correction within tracula. Tracula does not appear to recognize the format of my field maps in either dicom or nifti formats. However, as a work around I first did the field map correction outside tracula (using our wrapper script for epidewarp). Next I used this field map corrected image as the input diffusion image for tracula and set dob0 = 0 in my dmrirc file (so as to skip tracula's field map correction). This appears to be working. Eileen. > > -- > > Message: 5 > Date: Wed, 27 Aug 2014 13:51:06 -0700 > From: Eileen Moore > Subject: Re: [Freesurfer] trac-all -prep error field map error > To: "freesurfer@nmr.mgh.harvard.edu" > Message-ID: > lvufckbs+_061v7dctfc5t11pn0k4g9d-c...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Anastasia, I'm not sure how I can give tracula the phase difference maps, > can you provide an example? > > As a reminder, I've run a wrapper script around epidewarp which takes our > dicom images and converts them into a phase difference map (it is based on > the script that was authored by Doug Greve for the fBIRN consortium). > > In the tutorial dmrirc example I see only the 'set b0mlist' and 'set > b0plist' options, and am unsure where I could give it the phase difference > map. > > I've also tried converting the dicom magnitude and phase maps to nifti > format and inputting these into the dmrirc file but I am still getting an > error. (See attached log file). > > Thanks, > Eileen. > > > > > -- > > > > Message: 10 > > Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT) > > From: Anastasia Yendiki > > Subject: Re: [Freesurfer] trac-all -prep error field map error > > To: Freesurfer support list > > Message-ID: > > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > > > > Hi Eileen - All image formats that mri_convert (and thus any freesurfer > > program) can read will do, you don't need dicom. Try giving trac-all the > > phase difference maps you have and let's see what happens. > > > > Best, > > a.y > > > > On Wed, 16 Jul 2014, Eileen Moore wrote: > > > > > Hi Anastasia, > > > > > > OK - our imaging physicists had developed a wrapper script around > > epidewarp > > > which takes our dicom images and converts them into the phase > difference > > map > > > (it is based on the script that was authored by Doug Greve for the > fBIRN > > > consortium). It looks like the tracula script requires dicom images. Is > > > there a way for me to do epidewarp manually and then follow through > with > > the > > > remaining steps using trac-all? > > > > > > Thanks, > > > Eileen. > > > > > > > > > Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT) > > > From: Anastasia Yendiki > > > Subject: Re: [Freesurfer] trac-all -prep error field map error > > > To: Freesurfer support list > > > Message-ID: > > > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > > Hi Eileen - That step is run with the program epidewarp.fsl, > > > which you can > > > run on the command line to see the available options. The input > > > phase map > > > volume is expected to have either 2 frames (2 separate phase > > > maps) or 1 > > > frame (the difference phase map). This error from trac-all means > > > that it > > > found that your input phase map has something other than 1 or 2 > > > frames, so > > > it doesn't know how to handle it. > > > > > > Hope this helps, > > > a.y > > > > > > On Sat, 12 Jul 2014, Eileen Moore wrote: > > > > > > > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system. > > > I'm tyring to > > > > run tracula on some? images acquired from a GE scanner. I am > > > running into > > > > problems when I try to perform the registration-based > > > B0-inhomogeneity > > > > compensation, getting an error in the terminal output: "ERROR: > > > Unrecognized > > > > format of phase map". However, trac-all -prep runs fine when I > > > skip the > > > > B0-i
[Freesurfer] Tracula: missing or incomplete tracts
Hi - I'm having difficulty with missing or incomplete tracts most of my subjects. I'm hoping for suggestions on where I can look for data problems. The majority of my subjects have at least one missing/incomplete tract, but the specific problematic tract varies across subjects (e.g., one subject has a missing L.Uncinate; another subject has a missing Forceps Major; another is missing the ILF bilaterally, etc.). For my problematic tracts, the path.pd.nii.gz is a single line/curve rather than the diffuse volumetric distribution. I'm not sure how to correct this. I have checked my eigenvectors -- the lines appear to be pointing in the correct directions in my dtifit_V1 -- so I believe my gradient table is correct I've checked my images for motion via visual inspection and by excluding any subjects with dwi_motion outliers in AvgTranslation, AvgRotation, PercentBadSlices, and AvgDropoutScore. I inspected the nodif_brain_mask.nii.gz to look for chunks of missing brain and did not identify any problems here. I've tried increasing the number of control points for each tract. I'd very much appreciate any suggestions on how to troubleshoot next. Thank you, Eileen. ___ Freesurfer mailing list 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.
