Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

How to change the work path of freesurfer
by bowang21＠mail.ustc.edu.cn 27 Feb '12

27 Feb '12

Dear Nick Schmansky I am a beginner of freesurfer,and now I'm in trouble. I have install the VirtualBox to run freesurfer,but the disk space is not enough (11.0G).So I need to mount a disk to the system. And now I want to know how to change the working path of freesurfer such as SUBJECT_DIR. If you have some better idea to solve the problem,please tell me. Thanks in advance. Yours BoBO

3 2

Choosing a Contrast
by Allie Rosen 27 Feb '12

27 Feb '12

Hi All, I am trying to figure out the contrasts to use for a study. I am comparing age matched patients and controls (all female). The FSGD file has 4 columns, but I'm not sure how to make an appropriate contrast matrix. I can't seem to find an applicable example on the wiki. Any guidance would be appreciated. Thank you, Allison

2 1

Question about contrast matrix
by 林鄞 27 Feb '12

27 Feb '12

Dear all I have a question about the design of matrix. I have one group of two levels ( patient and control) and two continous variables (age and weight). And I want to know the difference of correlation of cortical thickness and the weight while controlling age between patient and control. My fsgd file is mainly like this: Class patient Class control Variables age weight I design the 1.mtx file as: 0 0 0.5 0.5 1 -1. I can not find the same sample in wiki. And I want to confirm whether my mtx file is right or wrong. If it makes mistakes, how to correct it? I really hope somebody can help me. Thanks for all! All the best, Lin

2 1

How to only do spatial normalization in FreeSurfer.
by Long 26 Feb '12

26 Feb '12

Dear all, I had EPI images and T1 image and the EPI images are already co-registered to T1 image in their native space. I also run 'recon' on T1 image. I'd like to try surface-based spatial normalization in FreeSurfer, so how can I only do the spatial normalization of EPI images in FreeSurfer, i.e., transform EPI images from native space to mni152 space, then I could have surface-based normalized EPI images. Best, Xiangyu

2 3

volume size
by Colin Reveley 25 Feb '12

25 Feb '12

Hi - I would really like to use a volume size greater than 256^3. I know of all the options and reasons. what I want is a white matter surface than has fairly evenly spaced nodes that are in approximate match to the voxels they enclose. the reason is to seed, track and target using FSL surface tractography. the brain is a 250um macaque, and it's 320 voxels long unfortunately. the structural and DWI are the same resolution and in register and acpc aligned. such a shame to waste. the freesurfer surfaces are imported into CARET and cross-registered to F99. but they keep their mesh if I want. work with another sample showed that node numbers and even coverage over the WM/GM boundary had a signifiant effect on the FSL metrics, with the original FS WM surface and derivatives yielding the best results over other meshes like F99's or anything made with surefit directly from a downsampled version of the data. that data I could fit into 256^3. I doubt that the nodes and voxels need to match perfectly, just ballpark and fairly even spacing. if I used a downsampled volume at 500um to make surfaces in freesurfer, maybe I could upsmaple the surfaces afterwards? but then the pial and white would have to be resampled independently and that's probably no good. If I have to resample the volume or apply a scaling transform the world won't end. In fact it will take less time to do probably. But it would be nice to use a larger size than 256^3 to take advantage of what I've got. best, Colin, Sussex

2 3

Frontal signal drop out
by Mahinda Yogarajah 24 Feb '12

24 Feb '12

Dear Experts, Sorry if this is a repost, but I was not sure it got posted. I have a few subjects that I want to salvage and use where there appears to be significant signal inhomogeniety in the last few frontal slices (see T1.mgz in attached figure 1). Despite the use of control points (placed with careful adjustments of windowing parameters), I still can't encompass all of the the gyri right at the front (see brainmask.mgz coronal slice in figure 2). I would really appreciate some advice on how to proceed from here. Is placing white matter voxels in wm.mgz a possible solution ? Or is there another solution ? Thanks. M

3 6

REPOST: MNI coordinates
by Antonella Kis 24 Feb '12

24 Feb '12

Hi, I am trying to find a way to get the segmentation/cortical label (to determine corresponding brain structures) in MNI space for a cluster for which I know the MNI coordinates. How can I do this? Many thanks. Antonella

2 1

Question regarding sig.mgh
by Antonella Kis 24 Feb '12

24 Feb '12

Dear All, 1)I would like to know what is the best way in catching the uncorrected clusters results from the sig.mgh for a structural study: Should I use the: mri_glmfit-sim \ --glmdir lh.GroupAnalysis_Thickness_15.glmdir \ --cache 2 pos \ --cwpvalthresh .99 \ --overwrite But in this case I am not getting all the clusters regarding their significance after correction by multiple comparison? I don't want the clusters from multiple comparisons just the uncorrected one. I am not sure why when I look to my clusters in QDEC I get a different p value for the uncorrected results sig.mgh that the one cached with the --cwpvalthresh .999 for example from QDEC for one cluster rostralmiddlefrontal in sig.mgh I got p =0.00338 while with the catche option and --cwpvalthresh .999 I got cwp 0.75890. I am doing something wrong? 2) If I know the MNI coordinates how I can get the location I mean the segmentation or annotation location of my clusters to the nears cortical label? Many thanks. AK

1 0

fsaverage error - too many levels of symbolic links
by Gibbard, Clare 24 Feb '12

24 Feb '12

Hi, I am running recon-all on several scans, but it is exiting with an error. I think the error is occurring because my symbolic link to fsaverage is self-referential. However, the symbolic link is generated automatically during recon-all so I cannot see how to correct it. I have tried deleting the fsaverage from my subjects directory and re-running recon-all, but this did not work. I can see that others have had this error before, but I can't see the solution. Are you able to help? I have previously run recon-all without getting this error. Thank you. ls -l /home/clare/freesurfer/freesurfer/subjects/fsaverage gives this: lrwxrwxrwx 1 clare clare 52 2012-02-17 08:27 /home/clare/freesurfer/freesurfer/subjects/fsaverage -> /home/clare/freesurfer/freesurfer/subjects/fsaverage Here is the error: #@# BA Labels lh Fri Feb 17 08:27:35 GMT 2012 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /home/clare/freesurfer/freesurfer/subjects; ln -s /home/clare/freesurfer/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject subject_001 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = subject_001 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/clare/freesurfer/freesurfer/subjects FREESURFER_HOME /home/clare/freesurfer/freesurfer Loading source label. Invalid argument ERROR reading /home/clare/freesurfer/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux clare-OptiPlex-990 2.6.35-32-generic #64-Ubuntu SMP Tue Jan 3 00:47:07 UTC 2012 x86_64 GNU/Linux recon-all -s subject_001 exited with ERRORS at Fri Feb 17 08:27:35 GMT 2012 Best wishes, Clare

2 2

Problem with preproc-sess per-session and question about registration
by Wiegand, Katrin 24 Feb '12

24 Feb '12

Hi, I have two short questions concerning motion correction using preproc-sess and registration files 1) Running preproc-sess using per-session as e.g. like this preproc-sess -per-session -fwhm 0 -sliceorder siemens -surface vpID lhrh -s vpID -fsd bold -mni305 should result in a "fmc" output stem, doesn't it? This however, this is not the the case (I received "fmcpr"), so I'm wondering whether the error occured (only) at the labeling stage or whether motion correction was indeed computed for each run separately (I also received register files for each run, i.e. in each bold/run directory, rather than "global ones" within the bold directory). Is this a known issue? 2) Furthermore I'd be very glad if someone could shed some light on the registration process (using fslregister-sess) for -per-run mc and the various register-files that are produced. In particular, I do not understand how the output of the statistical analysis of the functional data (averaged over all runs) is mapped onto the high resolution anatomical data, when every run is registered seperately. Which register file is needed in order the visualize the results? And what about checking the accuracy of the registration, do I have to check this for every run? I am using freesurfer Version 5.1.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0) on ubuntu 11.10 (64b). Thanks a lot in advance, Katrin

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