Don't smooth them! Smoothing creates partial volume effects. When you convert to nifti, you have to be careful to make sure that any DICOM intensity scaling is taken into effect; it is becoming more common these days. The only other thing may be to remove the gradient distortion from the MRI if possible (you would need to rerun recon-all)
On 1/20/2020 3:22 PM, Ferraro, Pilar wrote:
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Dear Freesurfer experts, I am starting a new analysis using PetSurfer to evaluate the effect of different PVC corrections on brain metabolism in a set of patients. I have already analyzed all the T1 MRI data using the normal stream, however I have never worked on PET data before. I have the original DICOMS from a static PET acquisition but I’d like to know more about the preprocessing steps needed for these PET data. I am thinking I should simply convert PET DICOMS to NifTI, normalize them to a standard template and then smooth them with 8- mm full width at half maximum Gaussian Kernel to obtain the input images for the PetSurfer analysis. Am I correct or should I add further preprocessing steps? Thanks,
Pilar
Il giorno 16 gen 2020, alle ore 6:00 PM, freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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Today's Topics:
1. Qdec and TkSurfer input boxes (Marcos Martins da Silva) 2. FreeSurfer analyses in MatLab (Graduate Imaging) 3. Re: Oval shape in average subject inflated (Marina Fern?ndez) 4. Segfault in mris_topo_fixer (Christian O'Reilly, Dr) 5. Re: Segfault in mris_topo_fixer (Hoopes, Andrew) 6. Segmentation Fault during recon-all using FLAIR Image (Swanson,Clayton)
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Message: 1 Date: Wed, 15 Jan 2020 14:02:26 -0300 From: Marcos Martins da Silva marcosm@hucff.ufrj.brmailto:marcosm@hucff.ufrj.br Subject: [Freesurfer] Qdec and TkSurfer input boxes To: freesurfer freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: CANXLKP7HxjOjLShobVkYr+eDGNuh+PksDM1Aio=9XgKm_NaXeg@mail.gmail.commailto:CANXLKP7HxjOjLShobVkYr+eDGNuh+PksDM1Aio=9XgKm_NaXeg@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click inside the box and even select the content but it seems read only: I can't change it. So it is impossible to see the scatter plot from a specific vertex inputing its number. Any clue about what happened and how to fix it? Thank you for your attention. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200115/11...
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Message: 2 Date: Wed, 15 Jan 2020 16:08:12 -0500 From: Graduate Imaging graduate.imaging@gmail.commailto:graduate.imaging@gmail.com Subject: [Freesurfer] FreeSurfer analyses in MatLab To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: CA+yW3sSV=E5M1_cbOJfecPMCeCePjtZy_isFL8vzmRMDX55Pfw@mail.gmail.commailto:CA+yW3sSV=E5M1_cbOJfecPMCeCePjtZy_isFL8vzmRMDX55Pfw@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Hello,
I recently ran a vertex wise analysis on two different projects the first had three groups with three co-variates that looked at if group membership was associated with brain volume. The second project had two groups with three co-variates looking at psychiatric x BMI interaction effect on brain volume. I'm interested in running ROI analyses in matlab to ensure the same matrices were used.
To run the ROI analyses I'm going to important the design matrix from the vertex wise analysis and use the fast_glmfit and fast_fratio commands as shown below: X = load('Xg.dat'); C = load('C.dat'); y = load('ROI.dat'); text file containing participant ROI values from the DKT atlas. [beta rvar] = fast_glmfit(y,X); [F pvalues] = fast_fratio(beta,X,rvar,C
My first question is the beta values that are calculated from fast_glmfit are unstandardized is there anyway way to have it compute standardized values?
My second question is when I ran the ROI analyses looking at the diagnosis x BMI interaction effect it outputs an array of beta values for each regressor. In addition to each groups beta value (for BMI) I'm interested in the beta value of the interaction (ie diagnosis x BMI). I was wondering how do i go about obtaining this? Would I have to create a new matrix with the interaction term included in it?
If so would the analysis essentially be one group with the diagnosis x BMI interaction term plus the three co-variates? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200115/10...
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Message: 3 Date: Thu, 16 Jan 2020 12:58:41 +0100 From: Marina Fern?ndez marina.fdez.alvarez@gmail.commailto:marina.fdez.alvarez@gmail.com Subject: Re: [Freesurfer] Oval shape in average subject inflated To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: CAALjZmeP2eKby4GGLJn_X6uOfCwPgNfnE3WUq5kmbv0-nqHi6Q@mail.gmail.commailto:CAALjZmeP2eKby4GGLJn_X6uOfCwPgNfnE3WUq5kmbv0-nqHi6Q@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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It works! Thank you very much Bruce! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200116/1f...
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Message: 4 Date: Thu, 16 Jan 2020 14:57:00 +0000 From: "Christian O'Reilly, Dr" christian.oreilly@mcgill.camailto:christian.oreilly@mcgill.ca Subject: [Freesurfer] Segfault in mris_topo_fixer To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: YQBPR0101MB10125047A377D0AD8F34D349E1360@YQBPR0101MB1012.CANPRD01.PROD.OUTLOOK.COMmailto:YQBPR0101MB10125047A377D0AD8F34D349E1360@YQBPR0101MB1012.CANPRD01.PROD.OUTLOOK.COM
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Hi,
I got the following error running mris_topo_fixer:
~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh INFO: assuming .mgz format verbose mode on (medium mode): printing warnings reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig... Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1) Surface Diagnostics: eno=0 (nv=43656, nf=87312, ne=130968) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect
The surface has 1 loops (X=0)
Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 1527 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ] ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 Segmentation fault (core dumped)
Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it?
Thank you,
Christian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200116/8a...
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Message: 5 Date: Thu, 16 Jan 2020 15:39:32 +0000 From: "Hoopes, Andrew" AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu Subject: Re: [Freesurfer] Segfault in mris_topo_fixer To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: BN8PR04MB56979DB2BBFD5A0BAB3E280EF9360@BN8PR04MB5697.namprd04.prod.outlook.commailto:BN8PR04MB56979DB2BBFD5A0BAB3E280EF9360@BN8PR04MB5697.namprd04.prod.outlook.com
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Hi Christian, if you send me that surface, I can take a look at what's going wrong.
best Andrew
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Christian O'Reilly, Dr christian.oreilly@mcgill.camailto:christian.oreilly@mcgill.ca Sent: Thursday, January 16, 2020 9:57 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Segfault in mris_topo_fixer
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Hi,
I got the following error running mris_topo_fixer:
~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh INFO: assuming .mgz format verbose mode on (medium mode): printing warnings reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig... Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1) Surface Diagnostics: eno=0 (nv=43656, nf=87312, ne=130968) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect
The surface has 1 loops (X=0)
Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 1527 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ] ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 Segmentation fault (core dumped)
Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it?
Thank you,
Christian
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Message: 6 Date: Thu, 16 Jan 2020 15:55:44 +0000 From: "Swanson,Clayton" Clayton.Swanson@colostate.edumailto:Clayton.Swanson@colostate.edu Subject: [Freesurfer] Segmentation Fault during recon-all using FLAIR Image To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Message-ID: A95D6E27-F818-45F7-9391-C5B130978013@colostate.edumailto:A95D6E27-F818-45F7-9391-C5B130978013@colostate.edu Content-Type: text/plain; charset="us-ascii"
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Hello FreeSurfer Developers, I am attempting to perform a recon-all using a T2-FLAIR image. I have already run this particular participant through recon-all with their T1 image without error. While running the recon-all using the T2 the process exited with error stating a segmentation fault.
Is there any way to run fix this problem on my end or better understand why this would be occurring?
I have uploaded the recon-all.log for your convenience.
Thank you, Clayton
________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Student Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson@colostate.edumailto:Clayton.Swanson@colostate.edumailto:Clayton.Swanson@colostate.edumailto:Clayton.Swanson@colostate.edu
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