Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

How to find mean LGI?
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 14 Feb '22

14 Feb '22

External Email - Use Caution Hi, I was hoping to extract mean LGI, similar to how there is a mean thickness. But the default LGI output includes the eTIV rather. What would the command be to collect the stats into a csv for this mean LGI? Get Outlook for iOS<https://secure-web.cisco.com/1dRo8XiQnC7RSEfM4uJvu8n55IiY3PyAp4VACtq0qGpKwZ…>

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hippocampal segmentation differences pediatric sample
by Aleksandra Lecei 14 Feb '22

14 Feb '22

External Email - Use Caution Hi, I'm new to this and was wondering if someone could help me out? I used a T1 preprocessed image (fmriprep), normalized to the NIH pediatric cohort 6 (13-18.5 years) template to do recon-all and then used the hippocampal segmentation tool v.7. I have two questions: a) wouldn't one expect the segmentation to be the same for different individuals if the normalized T1's are used (registration seems to be well aligned to the same space when checked in SPM but when looking into the .txt files the volumes are different)? and b) (how) do I need to use the -custom-tal-atlas flag to get the estimates back to the NIH pediatric atlas (cohort 6) and can I make masks from the hippocampal segmentations for ROI analysis in other software for this study population? Thank you!

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DICOM file organization
by krystaly 14 Feb '22

14 Feb '22

External Email - Use Caution Dear Freesurfer experts, There are a bunch of RAW DICOM files in my dataset. I recognize that the name of the images begins with Z, i.e. “Z01”, “Z02”… “Z8568”. After converting them into NIfTI format with mricron, it yields the name in this format: myFolder_MPRAGE_19770703150928_1.nii It’s rather inconvenient to have those names and have been stuck on organizing the images in different categories, i.e. T1, T2, M0, FLAIR and PCASL. I would like to have them named by subject numbers rather than a series of name and digits. For example, T2 DICOM images of a Subject 101 are named 101.nii under a folder called “T2”. Could you please advise if there is anyway categorizing the patients’ data into aforementioned categories automatically with Freesurfer? You help will be highly appreciated! Thanks. Best regards, Krystal

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ventricular volumes - freesurfer 6 vs 7
by Anik Dar 13 Feb '22

13 Feb '22

External Email - Use Caution Hi All, I have some datasets processed with freesurfer 6 and other datasets processed with version 7. Is it ok to combine the ventricular volume results from version 6 and version 7 ? Please advise, Thank you Ani

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[Help needed] recon-all log error
by HYE JUNG YOUN 13 Feb '22

13 Feb '22

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Building a model
by Marina Fernández 13 Feb '22

13 Feb '22

External Email - Use Caution Dear experts, We run the following analysis in Freesurfer: *Group* (2 levels) x *X1* (continuous IV) x *X2 *(continuous IV) + *Sex *(categorical covariate) + *Age* (continuous covariate) We exported the vertex with the maximum statistic after applying FWE correction to replicate the analysis in R. We want to make sure about the structure of the model to later do a Bayesian analysis using the same structure. We got significant results for most of our analyses but not for all of them, likely because we are not doing exactly the same thing. We have fitted several models in R, but the one that gave the closest results was the following: model <- lm (vertex ~ NewFactor (4 levels: Group*Sex) + X1X2 (resulting from X1*X2) * Group + Age*NewFactor, data=mydata) How should we introduce the interaction term in order to make the models fitted by Freesurfer and R comparable? Thanks a lot in advance, Marina

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Creating masks on a MNI averaged brain
by Lin Qiu 13 Feb '22

13 Feb '22

External Email - Use Caution Dear Freesurfer experts, My analysis is in FSL. But I wish to use the more detailed segmentaHA_T1.sh available in Freesurfer. I wish to avoid the time & resource to ‘recon-all’ all my participants’ T1 images, and only to transfer a set of masks superimposed on an averaged (MNI 1x 1x1 mm) brain – from Freesurfer to fsl. All my T1 images are pre-processed and registered using the FSL pipeline. So my first question is – Would it be sensible to create anatomical masks in Freesurfer directly onto the MNI standard brain image, rather that each participants’ T1, one by one? My second question is about running recon-all commands in parallel on a cluster – I read online that there is a -parallel flag in recent version of FS, so no need of installing a parallel package. However I was not able to use this flag in my FS 7.2.0. Please could you let me know how parallelization work on a cluster? Thank you very much! I look forward to hearing your advices! Best wishes, Lin -- Lin Qiu DPhil Student University of Oxford, Nuffield Department of Clinical Neurosciences John Radcliffe Hospital, Oxford OX3 9DU Email: lin.qiu(a)ndcn.ox.ac.uk<mailto:lin.qiu@ndcn.ox.ac.uk>

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rm: no match
by REEM ABU BAKR BAHATHIQ 13 Feb '22

13 Feb '22

External Email - Use Caution Hi all, I use a supercomputer to process my data When I run "recon-all –qcache", and after two days of processing there are a lot of Error messages saying "rm: No match." (although just this error message, no others). I'm wondering if this is something of concern, or something I can simply ignore. Thanks!

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-cw256 flag
by Harriet Dempsey-Jones 13 Feb '22

13 Feb '22

External Email - Use Caution Hi there, I am using AFNI to process some epi data. As part of this analysis, I am creating anatomical surfaces on which to project my data using recon-all in Freesurfer. My pre-processing in AFNI indicated that best alignment of my epi to anatomical image is achieved using a combination of affine and non-linear warping (3dQwarp in AFNI). So I was hoping to use this warped anatomical image from my experimental data to create a surface from with recon-all. I just tried to set this to run, and it errored and failed (see bottom of email) The gist appears to be that when it was completing the mri_convert stage it errored because the anatomical nifti image I had fed it, was not 256 FOV. It appears to be larger because I had to add some space to the image to rotate it during alignment. The error suggests using the flag -cw256 with recon-all, but I cannot find any documentation about how this works or what it does. I searched the forum archives as well, which came up with 60k hits, but none of them seemed to contain -cw256 when I control+f looking for it. Could someone let me know a bit more about this flag and whether it is ok to use for my purposes? I have included my recon-all code too for reference purposes. Please also let me know if there is anything glaringly wrong there, I am very new to fMRI analysis. Thank you for any help you might be able to give me! ERROR -------------------- mri_convert /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/rawavg.mgz /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 4078 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /scratch/inode/uqhdemp1/Surfaces/P00_FG/mri/orig.mgz... **************************************** ERROR! FOV=273.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux inode2.hpc.dc.uq.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s P00_FG exited with ERRORS at Tue Feb 8 22:13:53 AEST 2022 MY CODE -------------------------- #!bin/tcsh # Freesurfer start-up module load freesurfer # Set up vars set subj_init = FG set subj_num = P00 set subj = {$subj_num}_{$subj_init} set recon_use = (-all) # set recon_use = (-autorecon1) set anat = /scratch/inode/uqhdemp1/Fingertip_maps/{$subj}/{$subj}.results/{$subj_init}_uniden_avg_wholebrain_unpad_warped_3dQ.nii set base_dir = /scratch/inode/ set subj = {$subj_num}_{$subj_init} set expert_file = 1b_FS_expertfile ## 1. Freesurfer recon all recon-all $recon_use -s $subj -hires -i $anat -sd $base_dir/Surfaces -openmp 12 -expert $base_dir/Parent_scripts/Surfaces/$expert_file [cid:aa7c0bba-3c94-4eb9-a0b1-34aa283c77e9]

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Freesurfer with machine learning
by REEM ABU BAKR BAHATHIQ 13 Feb '22

13 Feb '22

External Email - Use Caution Hi everyone, Now that I have done the recon all preprocessing on my structural MRI data, I want to extract the volume and thickness of the gray matter and the surface area to use in a machine learning model. I find it difficult to determine which files I should take and is there any educational course that might help me for this plz share it with me . Thanks in advance

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