Freesurfer

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30082 discussions

Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII header
by Aloi, Joseph 23 May '16

23 May '16

Excellent, thank you! To do that, do I send an e-mail to the listserv with the log files attached or do I use the filedrop? yea, can you post the log file of both the successful and failing runs? On 05/19/2016 11:28 AM, Aloi, Joseph wrote: > > Hi Doug, > > No that’s not how I usually store my files- I have a folder for the > particular study that I am working on then the dicoms for each subject > in that study are stored in individual subject folders within the > study folder. > > I got a chance to look around the recon-all logs this morning for a > subject that I had successfully processed in the past (but that I get > the error when I try to process this same dataset now). From > comparing the recon-all log from when recon-all ran successfully > versus now, things are running fine up until it gets to MRI_convert. > However, it looks like things are actually starting to go haywire > during MRI_convert even before I get the warning about the ASCII > header and recon-all exits. It appears that MRI_convert is having > some trouble with extracting some of the information it needs from the > dicom file, resulting in the error that I posted. I know you guys are > busy, but would you be able to take a look at the log files? I’ve > only been using freesurfer a few weeks, so I would definitely > appreciate any insights you might have from looking at the log files. > > Thank you! > > I don't have any idea what is going wrong. I noticed that the file > that it is having problems with is here > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm > Do you really keep all your dicom files in that location? > > > > On 05/17/2016 11:47 PM, Aloi, Joseph wrote: > > Hi Doug, > > Sorry- I've added entire correspondence onto the end of this > e-mail. I don't think the disk filled up as I am on a 3 TB hard drive > and I still have ~2 TB of free space on my disk. Anything else you > think it could be? > > Thanks! > > Joseph Aloi > > Please remember to include previous correspondence otherwise we can't > > keep track of the problem! > > Eg, I don't have the previous email to see what the error was. Is it > > possible that the disk filled up? > > On 05/17/2016 09:49 AM, Aloi, Joseph wrote: > > > Hi Doug, > > > > > > Yes, you are correct- data I have previously processed without any > > > problems is no longer being processed. > > > > > > My version of freesurfer is 5.3.0; I only downloaded it a few weeks > > > ago so I have not changed my freesurfer version recently. > > > > > > Thanks! > > > > > > Joseph Aloi > > > Graduate Student, MD/PhD Scholars Program > > > Department of Pharmacology and Experimental Neuroscience > > > University of Nebraska Medical Center > > > > > > Neurobehavioral Research Assistant, Center For Neurobehavioral > Research > > > Boys Town National Research Hospital > > So the exact same data set is now generating an error whereas it ran > > smoothly before? What version of FS are you using? Did you change > versions? > > doug > > On 05/16/2016 09:49 AM, Aloi, Joseph wrote: > > > > > > Hi freesurfer experts, > > > > > > I have recently begun to use freesurfer to do structural MRI > > > analyses. I have been able to successfully process about 40 > > > structural scans with recon-all thus far, but starting a few days ago, > > > I started getting this error whenever I run recon-all: > > > > > > WARNING: file > > > /Users/alojos/Applications/freesurfer/subjects/sub_9999.dcm does not > > > contain a Siemens ASCII header > > > > > > has this file been anonymized? > > > > > > ERROR: cannot unpack mosiacs without ASCII header > > > > > > Darwin nerc130622.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan > > > 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 > > > > > > recon-all -s sub_9999 exited with ERRORS at Mon May 16 08:43:24 > CDT 2016 > > > > > > Here are a few of the troubleshooting steps I’ve tried to track down > > > the cause of the error: > > > > > > -- Re-run recon-all with a couple of scans from my dataset that I have > > > already successfully processed > > > > > > - - Re-run recon-all the same datasets but on a different computer > > > > > > - - Re-convert the scans from .ima files to dicoms in osirix, then > > > run recon-all > > > > > > > > > For all of these steps, I have gotten the exact same error message. > > > The files should be anonymized, since I used osirix’s “anonymize and > > > convert” function to generate the dicom files (the scans were given to > > > me as .ima files). > > > > > > Any suggestions on what to try next? > > > > > > Thank you! > > > > > > > > > Joseph Aloi > > > > > > The information in this e-mail may be privileged and confidential, > > > intended only for the use of the addressee(s) above. Any unauthorized > > > use or disclosure of this information is prohibited. If you have > > > received this e-mail by mistake, please delete it and immediately > > > contact the sender. > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > The information in this e-mail may be privileged and confidential, > > intended only for the use of the addressee(s) above. Any unauthorized > > use or disclosure of this information is prohibited. If you have > > received this e-mail by mistake, please delete it and immediately > > contact the sender. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <file://localhost/transfer/outgoing/flat/greve> > > > > The information in this e-mail may be privileged and confidential, > intended only for the use of the addressee(s) above. Any unauthorized > use or disclosure of this information is prohibited. If you have > received this e-mail by mistake, please delete it and immediately > contact the sender. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)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. Joseph Aloi Graduate Student, MD/PhD Scholars Program Department of Pharmacology and Experimental Neuroscience University of Nebraska Medical Center Neurobehavioral Research Assistant, Center For Neurobehavioral Research Boys Town National Research Hospital The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Deadline to sign up for Copenhagen Course is near!
by Allison Stevens 23 May '16

23 May '16

Hi everyone, There is just a week and a half left before the deadline to sign up for the FreeSurfer course being held in Copenhagen, Denmark on August 10th through the 12th. The deadline is June 1st. We still have a few places left! You can sign up for one here: https://fscph.nru.dk/registration.html This will be a 3 day course, very similar to the course we hold in Boston twice a year. The course will be taught by Lilla Zollei, Martin Reuter, Emily Lindemer, and myself. If you've had any trouble registering or have any questions, feel free to contact me or Melanie (fs-cph AT nru.dk) Allison

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hippocampal subfields analysis took 10 min
by Jiook Cha 23 May '16

23 May '16

Dear Eugenio, I had to run the hippocampal subfield segmentation analysis in Freesurfer v6 manually by running segmentSF_T1.sh program. When I call it through recon-all, it only processed the left hemisphere but not the right. The issue is that running segmentSF only took 10 min per hemisphere. I didn't use multicores. Although the analysis resulted in all the files correctly, I am just concerned if running this manually completed the analysis prematurely. Sincerely, Jiook ᐧ

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Lab coordinator position at the University of Michigan
by Adriene Beltz 21 May '16

21 May '16

Please see the ad below concerning a research position available in the new M(SD) lab at the University of Michigan directed by Dr. Adriene Beltz in the department of Psychology. Interested candidates should apply at http://umjobs.org/job_detail/125962/lab_coordinator and can reach Dr. Beltz at abeltz(a)umich.edu. Lab CoordinatorHow to Apply A cover letter is required for consideration for this position and should be attached as the first page of your resume. The cover letter should describe your interest in the position, relevant experience, and future goals. In addition, please provide contact information for three references. Job Summary The Methods, Sex differences, and Development Lab, or M(SD), directed by Dr. Adriene Beltz in the Department of Psychology seeks to hire a full-time Lab Coordinator. The goal of the research in the lab is to develop and apply novel quantitative approaches in order to reveal the ways in which the brain mediates biological and environmental influences on behavioral sex differences across development. To achieve this goal, data are collected from children, adolescents, and young adults using multiple methods, such as functional magnetic resonance imaging (fMRI), salivary hormones, observations of social interactions, daily diaries, cognitive tests, and online self reports. This would be an excellent position for a recent graduate seeking to gain additional research experience prior to graduate school. There will be training in multiple methods and opportunities for co-authorship on presentations and publications. The successful candidate will be highly-motivated, reliable, conscientious, and organized. Responsibilities* The Lab Coordinator will play an integral role in the establishment and functioning of the lab by fulfilling research, management, and supervisory responsibilities. - Lab management tasks (*20% time*) - Ordering supplies - Running and maintaining equipment - Organizing materials and resources - Overseeing the website - Research tasks (*60% time*) - Writing and maintaining Institutional Review Board protocols - Establishing data collection procedures - Developing study stimuli and data collection instruments - Creating project manuals and code books - Collecting, entering, processing, managing, and analyzing data - Supervisory tasks (*20% time*) - Training Assistants in Research (temporary positions) - Overseeing and supporting Assistants in Research assignments (e.g., data collection, coding, and entry) Required Qualifications* - High school diploma or Associate's degree - At least 1 year of experience - Excellent organizational, communication, problem-solving, writing, and computing skills - Familiarity with SPSS or similar software - Ability to work well independently and as part of a team - Attentive to details and able to manage simultaneous projects Desired Qualifications* - Bachelor’s degree in Psychology, neuroscience, or a related field - Experience with or an eagerness to learn fMRI methods, advanced statistics, programming (e.g., in Matlab or R), and online data collection - Research interests in the development of brain and behavioral sex differences Additional Information - One year term-limited position with excellent possibility of extension - Start date is negotiable, but August 1, 2016 is preferred Background Screening The University of Michigan conducts background checks on all job candidates upon acceptance of a contingent offer and may use a third party administrator to conduct background checks. Background checks will be performed in compliance with the Fair Credit Reporting Act. U-M EEO/AA Statement The University of Michigan is an equal opportunity/affirmative action employer.

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Extracting BOLD from a flattened surface
by Taha Abdullah 20 May '16

20 May '16

Hello Freesurfer Experts, Long story short--I would like to extract BOLD values from each TR across all vertices for one subjects flattened surface Following is a brief overview of my steps and at the end you can see where I am stuck. First, after *recon-all I* followed the steps to cut the lh inflated surface, saved as a patch, ran *mris_flatten, *converted patch into asc file. Second, I used read_patch.m to extract all spatial information and a net loss of approximately 10k vertices (127k to 116k) We had all functional images processed in FSL, the 4D file has 64x64x36x240 dimensions (voxels are 3.4x3.4x3.0). Next, co-registered the functional and anatomicals together via the following cmd: * bbregister --s cbp001_v1 --mov filtered_func_data.nii.gz --bold --init-fsl --reg dummy1.da*t. Afterwards, converted the volume to a surface using the following cmd*: mri_vol2surf --mov filtered_func_data.nii.gz --reg dummy1.dat --projfrac 0.5 --interp trilinear --hemi lh --o ./lh.func.vol2surf.mgh. *THe dimensions are 127027 x 1 x 1 x 240. Visually no problem when using* tksurfer cbp001_v1 lh inflated -patch /path to flattened patch/ -overlay /lh.func.vol2surf.mgh/ -timecourse lh.func.vol2surf.mgh;* click on the patch and shows the timecourse for that selected vertex. Using the View>Configure>overlay I can shuffle through the TRs to inspect the change in raw BOLD signal per vertex. I have been perusing the email web server searching for how to extract the hemodynamic waveform for each vertex across the flattened surface and ultimately will be using matlab to understand how the spatial transformation is happening. As well I have all the matlab files that seemed relevant to my query (read_surf.m, read_patch.m, and readMRI.m). I was hoping that I would be able to have a text file with all the vertices (127K not the flattened 116k) in rows and each column would have the TRs; I ran this command;* mri_segstats --slabel cbp001_v1 lh /home/share/freesurfer/subjects/cbp001_v1/label/lh.cortex.label --avgwf mri_seg_stats.dat --i lh.func.vol2surf.mgh*, output was the 240 TRs as rows and seems like the average global BOLD signal in the single column corresponding with each TR. Excuse my naiveness, I just recently (1 month ago) started using freesurfer and I feel like I have exhausted as much of the information available on the FS wiki and email server. Any information or advice would be great! I put the commands just to give an idea of my workflow (most of the command lines are from the email server or the FS Wiki) and if there are any issues with my steps please let me know so I can correct them before starting the group analysis. Best, Taha -- Taha Abdullah Department of Physiology Northwestern University Masters of Science Physiology and Biophysics, Georgetown University 2015

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Mult-Shell Tracula Help
by Kristina Jelinkova 20 May '16

20 May '16

Hello all, I had a question regarding the program Tracula. I have two different DTI sequences that I wish to run (b=900 and b=2000) but am unsure at which step I am suppose to merge the two sequences together. At this point, I have pre-processed each of the sequences separately using trac-all. Should I take each of the separate trac-all output data.nii.gz files, merge them, run bedpostX, and then run the ball-and-stick model fit on the new bedpostX output? Also, is there a way to use nii.gz files in the configuration file rather than a dcm list? Thank you in advance for your help!

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trac-all problem
by Zeng, Qi 20 May '16

20 May '16

Hi, I am running dti data with trac-all. I followed the command: trac-all -prep -c /Studies/*/DTI/dmrirc_subject but it exited with error "*Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension." * Before. there is another post about similar problem https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027802.… Dr. Yendiki suggested it could be because missing defined B0 in the dmrirc, but new version wouldn't need this (5.3, a new version?). If so, where can I obtain the B0 data? Can I compute from DICOM like nifti and bval, bvec? Best, Qi

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Re: [Freesurfer] Fwd: trac-all -path error
by Elijah Mak 20 May '16

20 May '16

Dear Anastasia Yendiki, I ran into a hitch while running trac-all -path and came across an identical problem where there was a segmentation fault. I have attached my error and log files. Loading initial proposal SD's from /subject/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt Processing pathway 2 of 18... Initializing MCMC I have also checked the aparc+aseg and aparc+aseg_mask (overlaid on FA; screenshot attached) as you have suggested, but I can't seem to find anything that would have compromised the -path process. What else could have gone wrong? trac-all -path works for other subjects. Thanks for your help. Best Wishes, Elijah

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Re: [Freesurfer] Inquiry a single curve problem for Tracula outputs
by Anastasia Yendiki 20 May '16

20 May '16

Hi Xiaofu - It's hard to tell but it looks like the brain mask (which comes from the structural data) is a bit too large in the temporal lobe, so it's possible that the structural-to-diffusion registration didn't go so well for this subject. You can check on this by overlaying the structural segmentation transformed into diffusion space (from dlabel/diff/aparc+aseg...) onto the FA map. Best, a.y On Sun, 1 May 2016, Xiaofu wrote: > Dear Anastasia or Tracula-group, > I have run Tracula and found there was only one single curve for some tracts. But others went well. I tried setting reinit parameter to 1 and > rerunning > "trac-all -prior" and "trac-all -path" but didn't get improved, e.g., the right UNC was a single curve (see attached). I also checked the two end point > set of right UNC (i.e.,endpt1.pd.nii.gz and endpt2.pd.nii.gz) (see attached) and found those end points were visually not correct when loaded to FA > image. I guess that may be the reason of the single curve problem. Is there anyway to fix this problem? Moreover, do you have any suggestions on the > tract statistics for those single curve tracts. I'd appreciate it if could take a look at it for me. If you need more files for the diagnosis please let > me know. > Looking forward to hearing from you. Thank you very much. > > Best, > Xiaofu > >

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Tracula Pathway reconstruction
by Peggy Skelly 20 May '16

20 May '16

Hi Tracula Experts, How do you determine if a pathway reconstructed well? I've been examining the merged pathways (<subj>/dpath/merged_avg33_mni_bbr.mgz) in freeview, and if the pathway looked too small when viewing with the default threshold, I would reinitialize those pathways. Most of the time, the new pathway would look ok upon re-inspection. A few pathways, however, still appear too small when viewed at the default threshold in Freeview, but at lower thresholds, they begin to look ok. I've encountered 1 pathway that still appears too small in Freeview, but the output in pathstats.overall.txt and pathstats.byvoxel.txt seem reasonable. On the other hand, its path distribution (path.pd.nii.gz) does not look like a distribution, but a single path -- there are a 38 voxels with values of 4000, and all others are 0. This doesn't seem right. What could cause this to happen? What objective measure can I use to determine if a pathway is reconstructed well enough? Thanks, Peggy

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