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30097 discussions

Masking in functional connectivity pipeline
by Rodriguez-Thompson, Anais 01 Jun '16

01 Jun '16

Hi FreeSurfer experts, I have a question about two specific steps in my fc pipeline. Since my seed is a single vertex, I convert the seed label to a mask, which I then smooth and binarize, and then convert to a volume file for fcseed-sess. 1) Is there way to directly convert a label into a cortical mask? Right now I use mri_label2label to create an outmask mri_label2label -s fsaverage -regmethod -surface -hemi -srclabel $SUBJECTS_DIR/{subject}/label/{label} -trglabel $SUBJECTS_DIR/{subject}/label/junk.label -outmask $SUBJECTS_DIR/{subject}/mri/{mask} cd $SUBJECTS_DIR/{subject}/label rm junk.label Is there a way to do this where I do not have to create another label in order to make a mask? 2) I can't figure out how to convert a cortical mask to a volume file (that I can use in fcseed-sess) using stable 5.3. I've tried to use mri_convert to create a volume file, but fcseed-sess errors out using this vol file (0 segmentations, core segmentation dumped) The command I use is: mri_convert $SUBJECTS_DIR/{subject}/mri/{mask} $SUBJECTS_DIR/{subject}/mri/{mask}.vol.mgz Currently, if I want to do this I need to switch to stable dev and run mri_surf2vol: mri_surf2vol -so $SUBJECTS_DIR/fsaverage1/surf/lh.pial $SUBJECTS_DIR/{subject}/mri/{mask} -subject fsaverage -o $SUBJECTS_DIR/{subject}/mri/{mask}.vol.mgz Is there a way that I can convert a surface mask to a useable volume for fcseed-sess in stable 5.3, rather than having to switch to stable dev? Thank you for your help! Anais Rodriguez-Thompson Clinical Research Coordinator Brain Genomics Laboratory Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617) 643-3215

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Re: [Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data
by Chung, Yoonho 01 Jun '16

01 Jun '16

Yes - I am interested in applying the monte carlo sim to my own model fit. Doug can you walk me through the steps I need to get this part done? When you say residuals, I am assuming that I need to supply a vector file of residuals after I fit my model to the smoothed data (eg. using mri_surf2surf --sval [concat thickness] --fwhm-trg [smooth level] etc. ) - correct? Since I don't have the --glmdir to supply, what are the other files or options that I need to manually supply for mri_glmfit-sim to run the correction? Thank you in advance!

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FC from resting-state
by Martin Juneja 01 Jun '16

01 Jun '16

Hello FreeSurfer experts, I am working on resting-state functional connectivity using freesurfer by following the instructions from: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… I made sure that the seed region (for ever subject) I am using is at the correct place on raw structural image. After running the analysis and looking at the RSFC maps, very few subjects showed very high FC at or close to seed region but for most of the subjects I am not getting high FC at/close to seed region. I would really appreciate any suggestion or tips on this e.g. what could be wrong during the analysis? Thanks. MJ

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mris_preproc - srcsubjreg
by Makaretz, Sara Johanna 01 Jun '16

01 Jun '16

Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as the default srcsurfreg when the target is not fsaverage - see below Thanks for any info! (not urgent) On 2016-5-24, 11:30, "Z K" <zkaufman(a)nmr.mgh.harvard.edu> wrote: >Good question, and I dont know the answer. mris_preproc is Dougs baby so >I suggest just posting this question to the list with "mris_preproc" in >the subject, and I bet he will give you the answer. > >-Zeke > >On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote: >> Hi Zeke, >> >> I am running some surface glms where targ is a patient surface. The help >> says --target TargetSubject (requires ?h.TargetSubject.sphere.reg), and >> I was getting errors because dev-default mris_preproc wanted >> mri_surf2surf to have srcsurfreg = >> $SUBJECTS_DIR/$srcsubject/surf/$h.$TARGSUBJ.sphere.reg >> >> But mris_preproc in 5.3 let me do target = patient surface with no extra >> surf reg files or extra flags to get mri_surf2surf to use srcsurfreg = >> $SUBJECTS_DIR/$srcsubject/surf/$h.sphere.reg >> >> I had been running this with 5.3: >> mris_preproc \ >> --target $TARGSUBJ \ >> --hemi lh \ >> --meas thickness \ >> --fsgd file.fsgd \ >> --out lh.output.mgh >> >> And I was about to email freesurfer@nmr but "for fun" tried adding >> --surfreg sphere.reg which got mris_surf2surf to use the right reg >> files. So now I'm selfishly trying to figure this out - do you know what >> prompted the switch from sphere.reg "opt-out" to sphere.reg "opt-in"? >> Aka why sphere.reg is non-default when the target is non-fsaverage? Did >> that make sense? I know there must be some reason, so I really want to >> know a bit more so I can stay sane when old scripts break. >> >> Thanks for any info! Sorry to bother you! >> Sara >> >> >> >> >> >> >> Outputs from the FS-dev one: >> >> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $ >> .... >> Src lh $TARGSUBJ.sphere.reg >> Trg lh sphere.reg >> .... >> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg >> $TARGSUBJ.sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg >> sphere.reg --etcetcetc >> .... >> ERROR can't find $SUBJECTS_DIR/$SRCSUBJ/surf/$TARGSUBJ.sphere.reg >> because I never made it >> >> >> >> Outputs from the FS-dev one with fsaverage as the targ subj: >> >> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $ >> .... >> Src lh sphere.reg >> Trg lh sphere.reg >> .... >> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg >> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --etcetcetc >> .... >> mris_preproc finds everything, runs no problem >> >> >> >> Outputs from the FS-5.3 one: >> >> $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ >> .... >> Src lh sphere.reg >> Trg lh sphere.reg >> .... >> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg >> --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg sphere.reg --etcetcetc >> .... >> mris_preproc exits with no errors because everything exists >> >> >> >>

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Questions about fsgd file & contrast
by jahanvi patel 01 Jun '16

01 Jun '16

Dear list, We have a question about the set up of the FSGD file. We have 1 group, 2 continued covariates (age & mintues), 1 discontinued covariate (sex) GroupDescriptorFile 1 Title G1V3 Class Main Variables Age Sex Minutes Input subject1 Main 30 0 1200 Input subject2 Main 40 1 180 My question is 1) How to enter the column "sex" in FSGD. Can I input 1 for Male and 0 for Female? 2) What would be the Main Contrast (regress out effect of sex & age)? (Null Hypothesis: the intercept/offset is different than 0 after regressing out the effects of age and sex) 3) If I want to correlate the continued variable (minutes) with the Thickness, is it correct in this way ? : 0 0 0 1 Thanks so much Jahanvi

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Postdoctoral Fellow in Pediatric MRI - NYC
by Mihaela Stefan 01 Jun '16

01 Jun '16

*The Cognitive Development and Neuroimaging Lab* in the *Division of Child and Adolescent Psychiatry in the Department of Psychiatry, Columbia University Medical Center and the New York State Psychiatric Institute* invites applications for a post-doctoral associate in the area of developmental cognitive neuroscience/pediatric MRI and child psychiatry, with a specific focus on obsessive-compulsive disorder and anxiety. Available resources include a 3.0T MRI scanner, a child-friendly mock scanner, analysis platforms based in MATLAB/UNIX, and servers for data processing and storage. The candidate will be expected to design, organize and conduct pediatric fMRI experiments, analyze behavioral and multi-band fMRI data, prepare manuscripts for publication, and participate in conferences. The successful applicant should have a doctoral degree in a field related to developmental cognitive neuroscience (e.g., cognitive neuroscience, neuroscience, developmental psychology, medicine or psychology). Individuals with a background in electrical engineering, biomedical engineering or computer science will also be considered, as appropriate. The successful applicant must possess excellent English verbal and written communication skills. Applicants are expected to have a very strong research background in the design and statistical analysis of functional brain-imaging experiments. Experience with SPM, FSL UNIX/LINUX and programming skills (MATLAB, C++; Python) is desirable and experience with HCP pipeline, MVPA, and connectivity analyses a plus. Approximate start date is between July 1 and September 1 2016. Successful applicants will be appointed at the New York State Psychiatric Institute. For consideration please send a statement of interest, a CV and a list of three potential referees via email to Rachel Marsh, Ph.D. marshr(a)nyspi.columbia.edu http://columbiapsychiatry.org/marshlab

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Tracula skip steps
by Jacobs H (NP) 31 May '16

31 May '16

Dear FreeSurfers, The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3. I have organized the data as mentioned on the wiki: For example: <subjID>/<dmri> dtifit_FA.nii.gz I have also filled in the configuration file, canceling out the things I don't need and then I tried to run: Trac-all -intra -c <configuration file> Unfortunately, it does not work, it says: dcmlist: subscript out of range I do not have the original files... is there a way that I can get the script working? Many thanks. Heidi

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mri_cc
by Arash Nazeri 31 May '16

31 May '16

Dear Freesurfer experts, Sorry for resending this post. mri_cc does not seem to be working properly to parcellate corpus callosum. As per one of the previous posts, there is a bug in the current release of mri_cc. However, the link provided in the same thread for an updated version of mri_cc is no longer existent. Our cluster runs on 64bit Ubuntu 14.04 systems. I'd be grateful if someone can post a new link for the corrected mri_cc. Thanks in advance. Cheers, Arash

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Extracting White Matter Structures without using Tracula
by Syeda Wajiha Maryam 31 May '16

31 May '16

Hello Freesurfer experts, I am looking to extract certain white matter pathways (for instance, the superior longitudinal fasciculus, uncinate fasciculus) with freesurfer which I believe are affected by Alzheimer's Disease. But it seems that these can only be obtained by performing tractography using Tracula. I was wondering if there was some other way to obtain the labels for these structures without having to do so? Thanks in advance. Regards, Maryam

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WM & GM Parcellation Edit
by Limachia, Gaurang (NIH/NINDS) [F] 31 May '16

31 May '16

Hi freesurfer community, We are checking to see the accuracy of our subjects’ white and gray matter parcellation. We have found that for some subjects the contour lines for white matter surface and pial surface are somewhat inaccurate, and have been making modifications using the tutorials. Specifically, we made changes to the white matter wm.mgz file; this however did not alter the contour lines. We also used control points, and were able to see changes to the white matter surface contour lines using this approach. How do you recommend that we proceed to obtain the most accurate results? Should we continue making changes to the wm.mgz file as well as adding control points, or is it sufficient just to add control points? I am attaching a screen shot which shows changes to the contour lines after we added control points. Best Regards, Shyam [cid:93CEA6F8-6B62-4483-985C-F540EDDBD2D7] [cid:C981D3FE-7C43-4073-A91F-F26CEDDC4145]

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