Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Can I extract GLM values?
by Thalhammer, Melissa 09 Jul '21

09 Jul '21

External Email - Use Caution Dear FS experts, I have run mris_preproc and mri_glmfit for group analysis as described in the docs. My current project deals with the analysis of cortical thickness of preterm- vs. term-born adults and I want to correlate the difference in cortical thickness between those two groups with gene expression data. Thus, I would need the group difference ROI-wise as values in a spreadsheet/text file to perform correlation lateron. I have used the following code with the --table flag and have used cortical thickness data extracted with aparcstats2table as input. Is there a way to extract the ROI-wise group difference, corrected for the covariates included into my GLM model? Best, Melissa Thalhammer

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mri_glmfit DOSS
by Dr. Cornelius Kronlage 09 Jul '21

09 Jul '21

External Email - Use Caution Dear freesurfers, for a morphometry study, I am comparing a single subject at a time to a group of controls. I would like to include age, gender (as a continuous variable for the sake of simplicity) and eTIV as "nuisance" regressors in the GLM. The FSGD looks like this: GroupDescriptorFile 1 Title SUBJECT1_vs_allControls Class Test Class Controls Variables Age Gender eTIV Input SUBJECT1 Test 50 1 1497422.2500 Input SUBJECT2 Controls 30 0 1709039.536815 Input SUBJECT3 Controls 29 0 1423097.816203 Input SUBJECT4 Controls 31 1 1524690.026713 ... When I try to run mri_glmfit I get the following error even though I specify DOSS: $ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...] gdfRead(): reading SUBJECT1_vs_allControls.fsgd WARNING: variable 1 is "Gender" which is often a discrete factor The proper way to handle discrete factors is to create classes. See https://secure-web.cisco.com/10ThHTirv10OEqbkasMHR-FObJ8JCIIzwnlckPdClcabJk… INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 28.6875 6.36611 1 Gender 0.46875 0.499022 2 eTIV 1.51444e+06 125811 Class Size and Means of each Continuous Variable 1 Test 1 50.0000 1.0000 1497422.2500 2 Controls 31 28.0000 0.4516 1514993.8589 ERROR: Class Test has 1 members. With 3 variables and using DODS, you need at least 4 members How do I get mri_glmfit to use DOSS, or do I have to specify the design matrix by hand in this case? Thank you! Best wishes Cornelius

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recon-all soft errors
by Rosalia Dacosta Aguayo 09 Jul '21

09 Jul '21

External Email - Use Caution Dear Freesurfer team, I am inspecting the different participants I have run recon-all -all and I have found different errors I would like to discuss with you before proceeding as I am new with this software. 1. I have found dura at some regions of the brain. I should use gcut or delete voxels? 2. I have found discontinuity in GM and what I should do with this (attached photo 2) 3. In photo 1, not sure at some regions were to consider wm as it is not clear for me...any suggestion with this one? I think it should be done with cp, right? Kind regards, Rosie

2 1

smoothing volume data extracted using aparcstats2table
by Ryan Bell, Ph.D. 09 Jul '21

09 Jul '21

External Email - Use Caution Dear Freesurfer Experts, I am wondering whether the extracted ROI volume data acquired when using the command aparcstats2table needs to be smoothed? I performed surface smoothing using surf2surf for cortical thickness data, but cannot find a way to smooth the volume data listed in aparcstats2table. Is it recommended that I do not perform smoothing? Thank You, Ryan ----------------------------------------------------------------------------------------------- Ryan Patrick Bell, Ph.D. Research Analyst, Department of Psychiatry & Behavioral Sciences 905 W. Main St., Suite 24-E Durham, NC 27701 Phone: (919) 681-3495 Email: ryan.bell(a)duke.edu<mailto:ryan.bell@duke.edu> Website: http://secure-web.cisco.com/1fzJIQLKPmbhrC2x32S5RRIKOnZE7eB318ehdee9qx2NWta… Twitter: twitter.com/HARPatDuke<https://secure-web.cisco.com/1K3qzDbdESi5BxKdIeeFsl0dti1McxRsbgZL6xE6fNf4Bc…>

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Re: [Freesurfer] Calculating group-wise Dice Similarity Coefficient and corresponding surface map
by Hye Min Shin 09 Jul '21

09 Jul '21

External Email - Use Caution Thank you for the response Bruce. I apologize for the confusion regarding surface map but what I was trying is that I wanted to create a surface file that contains dice coefficients for labels across the entire cortex. With your response, I think I can get the average dice coefficient for each label and hopefully create a surface map that visualizes dice coefficients on brain surface map. Would there be a way to create my own surface map with brain morphometry values that I created? Best, Julia Shin

3 2

Cortical thicknees normalization values
by Gabbo Ramírez García 09 Jul '21

09 Jul '21

External Email - Use Caution Hi freesurfer user. I have been working with some cortical thickness values of a control group to test some changes related to cognitive training. However, I have been hesitating about whether I have to normalize the cortical thickness values (as happens with subcortical volumes and ICV) or not. I have read a little about it and I understood that I could use the ICV or/and mean cortical thickness, but I didn't find a specific criteria to do or not this normalization. Any clue, recommendation, explanation or paper about this will be very helpful. Thanks in advance. *or reposting discussion of this question. Gabriel R.

2 1

Freeview filled in labels along with their outlines
by Pradyumna Bharadwaj 08 Jul '21

08 Jul '21

External Email - Use Caution Hi, In freeview, is it possible to view a collection of labels with different filled in colors, as well as their outlines? So, a combination of the filled in and outline only modes? Best, Prad

2 1

Fwd: Innis Lab postdoc position 2022
by Douglas N. Greve 08 Jul '21

08 Jul '21

-------- Forwarded Message -------- Subject: Innis Lab postdoc position 2022 Date: Thu, 8 Jul 2021 19:45:24 +0000 From: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> To: Innis, Robert (NIH/NIMH) [E] <innisr(a)mail.nih.gov> A postdoctoral position will be available in my lab starting in the first half of 2022. Please forward the attached advertisement to anyone who may be interested. The two major goals are translational studies of neuroinflammation (i.e., COX-1, COX-2, and TSPO) and indirect markers of cAMP signaling (via PDE4B and PDE4D). The studies extend from transgenic mice to monkeys and to patients, including those with depression or dementia. Stay safe and many thanks, Bob Innis ************************************ Robert B. Innis, MD, PhD Chief, Molecular Imaging Branch National Institute of Mental Health 10 Center Drive, MSC-1026 Bldg. 10, Rm. B1D43 Bethesda, MD 20892-1026 Tel: 301-594-1368 Fax: 301-480-3610 Email: robert.innis(a)nih.gov <mailto:robert.innis@nih.gov> Branch Administrative Manager: Elizabeth Alzona Tel: 301-594-1089 Email: alzonae(a)irp.nimh.nih.gov <mailto:alzonae@irp.nimh.nih.gov> Molecular Imaging Branch website<https://secure-web.cisco.com/1ArBJjYhVhrUft9gNOaLCuNtmSeJ1qPEnHkkGF7qzP9gVj…> ************************************ ____________________________________ LEGAL CONFIDENTIALITY NOTICE: This email message (including all attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.

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BERT - Example of segmentation
by Rosalia Dacosta Aguayo 08 Jul '21

08 Jul '21

External Email - Use Caution Dear Freesurfer team, It is my first time editing wm segmentation (white matter segmentation errors + topological errors). I wonder if there is a good tutorial on which I could rely. Also, I have read there is an example of segmentation that comes with FreeSurfer that is called Bert. I think it would be great to have it so I can look at it as a good example. Your help on this is very much appreciated Kind regards, Rosie

2 5

Interscanner variability
by AJ 07 Jul '21

07 Jul '21

External Email - Use Caution Hi, I am running Freesurfer on longitudinal datasets all obtained on 3T scanners. Unfortunately, many of the MRIs were done on different scanners, Phillips and GE. Would longitudinal pipeline help reduced scanner variability or should I process crossectionally each time point separately and normalize these time points with eTIV? Many thanks AJ

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