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wmparc.mgz
by Pedro Rosa 01 Aug '13

01 Aug '13

Hi, Is it possible to obtain the wmparc.mgz file without running all steps from autorecon2 and 3? Thanks, Pedro.

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[tracula] error running trac-all -prep
by Borsodi Florian 01 Aug '13

01 Aug '13

Hello, I have been trying to run tracula on my data and i keep getting the same kind of error repeatedly. For my imput I am using dicoms from a Siemens scanner with a stadard diffusion protocol. However, tracula cannot read the bvec and bval data out of the dicom header. Therefore, I implemented bvec and bval files into the config file. After doing so, I got the error which says that tracula cannot find the "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. I have tried many options, but still cannot find a solution. I am hoping to get some troubleshooting help. I have atteched my log- and config- files, as well as my bvec and bval files. To uphold patient confidentiality, I have encode the name patient's data as "AAAAAA". I believe the problems are the bvec and bval files or their structures. The log-file lete me assume this, especially the lines 202 - 205, 264 - 268 and 1480 - 1484. Thank you in advance for your help, and your speedy response. With kind regards, Florian Borsodi Department of Neurology Medical University of Graz

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white matter surface crosses over pial surface
by Maia Pujara 01 Aug '13

01 Aug '13

Hi, I recently came across a subject whose white matter surface cuts through the pial surface for about 10 slices bilaterally (see attached screenshot). I think it may be a problem with the white matter mask, but I'm not sure. Are there any recommendations for troubleshooting this particular problem? Thank you, Maia

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Can I include this pre- vs. post- patient dataset?
by Qi Wu 01 Aug '13

01 Aug '13

Hi Freesurfer experts, I have a difficult decision to make and I don't know which direction is better. Your opinions are needed. We are planning a paper on the treatment effects of a drug on the cortical plasticity in a group of patients ( the pre- vs. post- design). It has been a huge challenge to recruit patients for this subject. So far, after 3 years of active recruitment, we have only 13 complete set of pre- vs. post- data. But , we have another set of data which was collected at the earliest stage of the project with slightly different parameters. The main difference is the in-plane resolution; those 13 patients have a 1mm*1mm*1mm isovoxel resolution and that particular patients has a 1mm*0.86mm*0.86mm resolution. To include the subject increases the power of the pre- vs. post analysis, as we are working in the range of relatively low S/N (only 13 pairs). We also know that we are open to attack if we include the subject with different scan parameters. Anyone knows how big the impact would be. Is there anyway to estimate the impact? Is it easy to get away with the potential critique about this issue? Is it a must-not case? Many thanks Keith Postdoc fellow Toronto Western Hospital Canada

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TR,TE,TI,FA variability w/ mri_ca_train
by Mark Plantz 01 Aug '13

01 Aug '13

Hello freesurfers, I currently have a series of images with various TR,TE,TI,FA values. I would like to use mri_ca_train to create a .gca atlas based on these segmented volumes. Unfortunately, they all have slightly different control parameters (TR,TE,TI,FA). Is there any way around this problem, or would it be best to break the subjects into multiple groups with the same control parameters? Here are the various parameters: [each row is a subject] *TR* *TE* *TI* *flip angle* 9.38 3.86 450 12 9.34 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.34 3.86 450 12 9.44 3.87 450 12 9.39 3.86 450 12 2065.98 7.61 886.92 90 9.45 3.89 450 12 9.41 3.87 450 12 9.41 3.87 450 12 9.42 3.91 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.44 3.86 450 12 9.44 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.34 3.86 450 12 9.34 3.86 450 12 9.39 3.86 450 12 1900 2.6 900 9 1900 2.6 900 9 1900 2.6 900 9 9.41 3.87 450 12 9.41 3.87 450 12 9.41 3.87 450 12 1900 2.6 900 9 9.41 3.87 450 12 1900 2.6 900 9 1900 2.6 900 9 Thank you in advance. -Mark

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Recon-all errors
by Stéphane Poulin 01 Aug '13

01 Aug '13

Dear Freesurfer experts, Regarding recon-all troubleshooting, my understanding is that you can edit wm and complete the pipeline with recon-all –autorecon2-wm. Similarly you can complete the pipeline with recon-all –autorecon2-pial if there is a problem with the pial surface. If there are both white matter and pial surface edits, is there an “efficient” way to correct for both and complete the pipeline. Thanks, Stephane

2 1

Cerebellum Subcortical edits
by Michael Kranz 01 Aug '13

01 Aug '13

Hi guys, I was just wondering approximately how often the aseg volume will need manual edits. I know the tutorial says very rarely but I noticed that most of my subjects have non-brain matter (I think) incorrectly labelled as cerebellum. Attached is a pic of what I mean.[image: Inline image 1] Thanks, Mike

3 4

type of errors
by clelia pellicano 01 Aug '13

01 Aug '13

Dear freesurfers, I have run recon-all -all on some subjects and I got these errors I never had before. mri_ca_register -invert-and-save transforms/talairach.m3z GCAMread(transforms/talairach.m3z): invalid version # 7573008809984.000 Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux wmen-ps2208 2.6.32-358.14.1.el6.x86_64 #1 SMP Mon Jun 17 15:54:20 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CHWI exited with ERRORS at Thu Aug 1 10:50:29 BST 2013 For another subject: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0747, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux wmen-ps2208 2.6.32-358.14.1.el6.x86_64 #1 SMP Mon Jun 17 15:54:20 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ALTH exited with ERRORS at Wed Jul 31 15:34:36 BST 2013 And for another one, I got just this: mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse Could you help me? Thank you so much Clelia

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unpacksdcmdir error for resting state fMRI
by Eli Fredman 31 Jul '13

31 Jul '13

Hi all, I am following the FsFast tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkt…) for resting state data and I am stuck at the unpacksdcmdir step. When I try and run the command I get an error that says "ERROR: Run ## does not exist in session." I've tried several different combinations of numbers that I thought might be the run ## but I haven't had any success. All the data I am using are in .IMA format, not .dcm (ex. 000001.IMA 000002.IMA 000003.IMA...000140.IMA), so I am unfamiliar with how to find the scan acquisition number. Thanks for the help! P.S. Are there any good video tutorial's out there for resting state data? I have never done any fMRI analysis until now. -- Eli Fredman, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6118 Cell: (314) 952-8098 Fax: (617) 525-6150

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defect of cerebellar segmentation in the inferior part
by charles laidi 31 Jul '13

31 Jul '13

Dear Freesurfers, **** ** ** I am experiencing recurrent issue while performing cerebellar segmentation on T1 images.**** ** ** These are the characteristics of the acquisition:**** **§ **T1: field of view (FOV) = 230 mm**** **§ **repetition time (TR) = 1140 msec**** **§ **echo time (TE) = 4.38 msec**** **§ **matrix size 256 × 256** **§ ***interpolated to 512 × 512* **§ ***yielding an in-plane voxel size of 0.45 mm × 0.45 mm***** **§ **slice thickness of 0.9 mm**** ** ** After recon-all (ended without errors) I always end up with the same error in segmentation (see attached file) : there is the same defect of segmentation in the inferior part of cerebellum. **** ** ** Are you aware of any way to correct this defect ? (I think this might be related to the low resolution of my images)**** ** ** Thank you for your time. **** Best regards**** Charles**** **

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