Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Cross sectional analysis of a longitudinal data
by Kasper Jessen 29 Mar '16

29 Mar '16

Dear FreeSurfer experts, We have a longitudinal study design with up to 5 time points. However, we both want to do a baseline cross-sectional analysis and later a longitudinal analysis. All subjects have been run through the longitudinal pipeline (only the base was edited). We want to start analysing baseline cross-sectionally using QDEC. I have read through the wiki guides but would like to make sure that we are doing it correctly. We have done/plan to do the following: 1. The [CROSS], edited [BASE] and [LONG] is processed. 2. We will create a qdec table called qdec.table.dat. However, because we want to use the improved longitudinal runs [LONG] (i.e., because the [BASE] has been edited] the first column in the QDEC table (i.e., fsid) has been changed to include the longitudinal names (please see below). In addition, we have included the line *SUBJECTS_DIR /my/path/to/subject/data* to let FreeSurfer know that it is the longitudinal directories that should be used (is this the correct why to let FreeSurfer know that it is the "longitudinal runs" which should be used?). SUBJECTS_DIR /my/path/to/subject/data fsid Gender Group Age d115a.long.d115_base 1 1 19 d120a.long.d120_base 0 1 22 ... 2. We transfer the default fsaverage to the subject directory. 3. To presmooth the data onto the target we run the following command: *recon-all -long <tpid> <baseid> -qcache* When the above steps are done we plan to load it into QDEC. Is the above steps correct for doing a cross-sectional group analysis in QDEC? Best regards, Kasper Jessen MD, PhD student

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Error of invalid license file
by Yuan Lin 28 Mar '16

28 Mar '16

Hello, I installed the Freesurfer tool several months ago. Today when I run the "recon-all" command, it showed the error "ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment." I have created a .license file and copied the following information from the email. Y***(a)hotmail.com 26162 *C0m0U2INd.0M FS1DlaVbYasqE But the error still exits. I don't how to solve it. Can anyone help me? Thank you so much. Best Lin Yuan

1 0

Pial segmentation error
by Deniz Ozgen 28 Mar '16

28 Mar '16

Hi everyone, We have been having consistent errors, where the extreme left and extreme right of the brain are mis-segmented. Basically, it looks like the intensity normalization is not working well. I'm sending a screenshot to illustrate the problem. We added control points to fix the errors before, but this one seems like a lot of work. Is there a solution you can offer? Such as changing parameters for segmentation etc. FYI: image is acquired on a Skyra scanner with FA 9 degrees, TI 930, TR 2300, TE 2.39. We may be able to change the parameters in the future, but we still need to get these scans processed. Thank you. [image: Inline image 1]

1 0

whole hemisphere is yellow
by Miracle Ozzoude 28 Mar '16

28 Mar '16

hello doug, i performed a group analysis and after correction for multiple comparisons when i tried to load the corrected clusters the whole hemisphere was completely yellow. what should i do? Best, Miracle

3 15

initial processing in devel 6.0 version and final stats processing in stable version 6.0?
by Lara Foland-Ross 28 Mar '16

28 Mar '16

Hi Freesurfer experts, We'd like to begin a cortical thickness and hippocampal subfield analysis in the most recent devel version of FS. Can you please confirm that we will we be able to run the analysis of these data in the final stable release of 6.0? Thanks, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

3 2

(no subject)
by stdp82＠virgilio.it 28 Mar '16

28 Mar '16

Hi,I'm wondering whether the FS-FAST performed bandpass filtering. Stefano

2 1

improving white/grey segmentation in recon -all for better volume estmation
by Ramtilak Gattu 28 Mar '16

28 Mar '16

Hello all, We have run recon -all on some healthy control subjects T1 images but we found out that the gray-white segmentation on half our subjects is bad and it leads to increased white matter volumes and decreased gray matter volumes. I have included a snap shot showing the difference in segmentation from bad to good for 3 cases https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts… . The parameter in the sequence are TE=4.92 ms, TR=19 ms, Flip angle =20 degrees. and use a snapshot one slice to show the good CNR. We are using Freesurfer version 5.3. Thanks Regards Tilak.

3 5

FS-FAST bandpass filtering
by stdp82＠virgilio.it 26 Mar '16

26 Mar '16

Hi,I'm wondering whether the FS-FAST performed bandpass filtering. Stefano

1 0

getting started
by david sandeman 26 Mar '16

26 Mar '16

Hi I am a neurosurgeon working with robotics I have recently purchased a new macbook pro, running version 10.11.3 of OS X El capitan, speficially to run free surfer and other sofrtware designed to enhance my 3D segmentation capability The downloads I have tried only allow me to load freeview automatically. can you advise me how to set free surfer up on my mac or refer me to a download that will load the software automatically kindest david sandeman

1 0

Is it possible to use the mris_make_face_parcellation with the ico6 mesh?
by Michael Waskom 25 Mar '16

25 Mar '16

Hi Freesurfers, I'd like to use mris_make_face_parcellation to downsample an individual subject's surface mesh to a resolution similar to fsaverage6. My understanding is that mris_make_face_parcellation should let me do this, and it does what I expect with ic3-5. However when I run it with ic6 as the target, it fails: [surf]$ mris_make_face_parcellation lh.sphere $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot Reading lh.sphere Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri parcellating hemisphere into 40962 units INFO: CTABunique() could not find a unique set in 10 tries INFO: CTABunique() could not find a unique set in 100 tries ERROR: could not find a unique color table I don't really care if the colors themselves are distinct, and it should be possible to just programmatically generate a valid color table (since 255 ^ 3 > 40962). I thought that providing a colortable with unique values through the -ctab option might work, but looking at the source code it seems that option will *write* a colortable, not read one. So, is there any way to accomplish the downsampling I want? Thanks in advance, Michael

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Freesurfer March 2016