Freesurfer

freesurfer@nmr.mgh.harvard.edu

24 participants
30076 discussions

Seeking pass code
by FELICITY SIMPSON 01 Jun '22

01 Jun '22

External Email - Use Caution Hi there, I am hoping to access the pass code required to open my .ova.7z file as a 7zip file. Thank you in advance for your assistance, Felicity Simpson, University of Newcastle,

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samseg2recon error / missing files
by Jacob Levenstein 01 Jun '22

01 Jun '22

External Email - Use Caution Hello Freesurfer team + users, I am looking to run segmentHA_T1.sh following samseg + samseg2recon, and came across this previous thread where it seemed to workout: https://secure-web.cisco.com/1u2xTmmnCUaxQQuSTDRURAlZzdIaStC1AkxmbcmeQ18lFv… Given that I am writing in, I have not yet gotten this to run properly... Below is my samseg command: samseg --t1w ${subject}_${ses}_T1w.nii.gz --sd . --s ${subject}_${ses}_samseg --refmode t1w --threads 16 --parallel >From the log file, samseg seems to run correctly, but once it reaches the samseg2recon steps, I receive the following error: ln -sf orig.mgz rawavg.mgz ERROR: ln -sf orig.mgz rawavg.mgz ERROR: samseg2recon --s ${subject}_${ses}_samseg --tmpdir ${SUBJECTS_DIR}/${subject}_${ses}_samseg/mri/samseg/tmp.pyBLVF/tmp.mergeseg --cleanup If I then (re)run samseg2recon on the samseg directory (see cmd below) , I can execute the failed lines, and this script completes without error. samseg2recon --s ${subject}_${ses}_samseg However, when I then try to run: segmentHA_T1.sh ${subject}_${ses}_samseg, I receive the following error: Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all? As the error message correctly states, within that subject's dir, I do not have an mri/norm.mgz or mri/wmparc.mgz. I do have an mri/samseg/transforms/samseg.talairach.xfm, but it is not in the scripts expected location/naming convention. If it is helpful to know: i. Running recon-all then segmentHA_T1.sh completes without error... ii. Copy over the mri dir from the recon-all to the samseg subject dir, then running segmentHA_T1.sh also completes without error... iii. I am running Ubuntu 20.04.4, freesurfer-linux-ubunu18x86_64_-7.2.0-20210721 Any idea what may be going wrong with samseg/samseg2recon? I am happy to use the workaround listed above, but I suspect there may be a more efficient way, and or unintended implications when mixing and matching recon-all and samseg...? Thank you for your help and insight! All the best, Jacob

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fmcpr.up.sm5.mni305.2mm.nii.gz label
by Mingyang Xia 01 Jun '22

01 Jun '22

External Email - Use Caution Dear Freesurfer expert: I am Mingyang Xia. I use freesurfer to preprocess the fmri data and map to the fsaverage and generate a file named fmcpr.up.sm5.mni305.2mm.nii.gz. I want to get the label of this file however I could not find the label in the fsaverage folder. Could you give me some advice? Thank you Mingyang Xia

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extracting BAs in freesurfer
by Sam W 01 Jun '22

01 Jun '22

External Email - Use Caution Hello! Is it possible to extract brodmann areas not included in the aparc? For example, BA9, BA10 and BA32? Thanks! Best regards, Sam

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Surface normalization
by Rafael Navarro 01 Jun '22

01 Jun '22

External Email - Use Caution Hello FreeSurfer Developers, I am building a brain age model from the stats extracted with FreeSurfer. I tested my model normalizing volumes by eTIV, which I think is the recommended, and surfaces by WM total surface. For surfaces, I haven't found any recommendations. I am getting better results by using the features without normalization. From what I have read, volume normalization clearly should be performed, but I am in doubt about the surface normalization. Although, the surface is different depending on head size and along with lifespan, I am not sure if all cortex surfaces evolve the same way, and therefore that normalization might be adding noise to my results. Then, is it correct to normalize my surface features by the total WM surface? Does anybody know any reference that talks about the topic or have done similar work? Thank you for your support ----------------------------------- || Rafael Navarro González || Ph.D. Student || ETSI Telecomunicación || Universidad de Valladolid || Campus Miguel Delibes || 47011 Valladolid, Spain || e-mail: rafael.navarro(a)uva.es || Phone: +34 672 394 294 ||_________________________________ -----------------------------------

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Now accepting applications for MSc Applied Neuroscience at Royal Holloway, University of London
by Joe.Bathelt 01 Jun '22

01 Jun '22

External Email - Use Caution **APPLY NOW FOR MSC APPLIED NEUROSCIENCE IN ONE OF HIGHEST RATED PSYCHOLOGY DEPTS IN THE UK** MSC APPLIED NEUROSCIENCE - Department of Psychology, Royal Holloway, University of London * You can gain a unique insight into the ways that Neuroscience techniques can be used in real world settings – with hands-on experience across a range of applied neuroscience techniques taught by leading experts * Exciting career opportunities such as user experience, digital design and marketing, immersive technology, data science, research or a PhD! * Applications encouraged from undergraduates in related Psychology/Cognitive Science/Biology/Computer Science/Physics/Mathematics * https://secure-web.cisco.com/1Ks48yyW-4KxFhlRXaR4GBM2FwuZSePvnHvWq80M5uZutu…<https://secure-web.cisco.com/1Pb57hF7a9UBX7ENNpSFL9SB9z3tI4NaNEK_CJjY_dgbjH…> This email, its contents and any attachments are intended solely for the addressee and may contain confidential information. In certain circumstances, it may also be subject to legal privilege. Any unauthorised use, disclosure, or copying is not permitted. If you have received this email in error, please notify us and immediately and permanently delete it. Any views or opinions expressed in personal emails are solely those of the author and do not necessarily represent those of Royal Holloway, University of London. It is your responsibility to ensure that this email and any attachments are virus free.

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Custom LUT
by Benjamin Deck 31 May '22

31 May '22

External Email - Use Caution Hi freesurfer experts, I am attempting to create a custom LUT from a parcellation I created. I have projected the labels into the subject's volume space and then concatenated all of these volumtes together using: mri_concat --sum --f vols.txt --o sub_vols.mgz When I visualize these on the subject's t1w the number of ROIs looks approximately correct (n~105). However, my custom LUT seems to be incorrect. Not sure how that is. I used the FreesurferLUT as my template and added new colors and changed names of each row to match my file names (excluding the .mgz). Here is my custom LUT 0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 5 5 5 5 2 Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 25 5 25 0 3 Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 25 100 40 0 4 Net_11_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 70 130 180 0 5 Net_12_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 100 100 0 0 6 Net_12_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 196 58 250 0 7 Net_12_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol 100 25 0 0 8 Net_12_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol 120 70 50 0 9 Net_13_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 220 20 10 0 10 Net_13_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 220 20 100 0 11 Net_13_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol 180 40 120 0 12 Net_13_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol 122 186 220 0 13 Net_13_ROIs_3_lh_native_sm6_sm6_dil2_lh_vol 140 20 140 0 14 Net_13_ROIs_3_rh_native_sm6_sm6_dil2_rh_vol 12 48 255 0 15 Net_13_ROIs_4_lh_native_sm6_sm6_dil2_lh_vol 20 30 140 0 ------and it goes on for 105 indices. here is my list of volumes Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_19_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_2_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_2_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_11_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_2_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_12_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_2_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_12_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_3_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_12_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_3_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz -------and so on. Below I show that you can load each volume onto the brain and pick individual colors. [image: image.png] However, when I load the concatenated brain and load my custom image. All of ROIs get listed one of two ROIs. [image: image.png] Any guidance on this odd behavior would be much appreciated. Thanks, Ben OS: Windows--WSL2 Ubuntu 18 FS version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/19Zn9eBKlEcFDurLHH9K8qOmPXm76HWXsKoN-XxABNV__4…> Virus-free. http://secure-web.cisco.com/17nfhwzVH4FamivxxfM5csvgLADzPjVc-AdC_7JKlsJRQMF… <https://secure-web.cisco.com/1E0laxvnp9bhVNgWasuocl4hqSjGHLHVu2yD3TqEvK6dfc…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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mri_normalize issues, Version 7
by Zoe O'Brien-Moran 31 May '22

31 May '22

External Email - Use Caution Hello FreeSurfer developers, I am attempting to run the mri_normalize function on T1 MPRAGE data and some of my subjects get an error: Iterating 2 times ------------- 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed This error comes up with some subjects but not others in the group with the same acquisition details. It is cross vendor (it has come up for both Siemens and Philips). Strangely enough, when I gave the data to someone else to run on their end, mri_normalize worked just fine... they are running FreeSurfer 5.3.0. On my own computer, running freesurfer version 7, I can get it to work by changing the orientation using mri_convert... though most subjects work with the original input orientation, and I would prefer not to have to do what feels like an arbitrary orientation change. Do you know why this could be happening? Were there any changes made to the mri_normalize function between v5.3.0 and v7? Thank you so much for any advice. Zoe O'Brien-Moran

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convert surface overlays to atlas
by Benjamin Deck 31 May '22

31 May '22

External Email - Use Caution Hi there freesurfer experts, I am fairly new to freesurfer. I am attempting to convert freesurfer overlay files and eventually create individual-specific annotation files which will then be used to create a segmentation file to be used for drawing white matter tracts. When I run mri_info on the overlay files I get the following: Volume information for Net_10_ROIs_1_lh.mgh type: MGH dimensions: 253237 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 253237.000 dof: 1 xstart: -126618.5, xend: 126618.5 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 1281.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.5000 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1.0000 0.0000 0.0000 -126618.0000 0.0000 1.0000 0.0000 1280.5000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: 1.0000 0.0000 0.0000 126618.0000 0.0000 1.0000 0.0000 -1280.5000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 My initial thought was to run mri_label2label --> mri_label2vol --> mris_label2annot --mri_label2vol --> mri_concat = segmentation in native volume Running WSL2 Ubuntu 18_x86_64-7.2.0 FS: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Any guidance would be greatly appreciated. Thank you! -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1kz89t9S4HXvtMVxUekw-dPXLzzUcmmP6UBXoFUZuORVdR…> Virus-free. http://secure-web.cisco.com/1WixBPHZpnyB5-Xayd80a9TON-TvjqvK-WeaqazG-xtlOgj… <https://secure-web.cisco.com/1hU1RdFIRZigHPH9QSngZUY6qgxOLWWme7Djq567riRfsJ…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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convert .reg.lta linear transform to an ITK transform for 3DSlicer
by Gonzalo Rojas Costa 31 May '22

31 May '22

External Email - Use Caution Hi: How can I convert a .reg.lta linear transform to an ITK transform for 3DSlicer? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/13TZ07AstA_Q_lsIF4aiCFiJWD-gpdMOlT0cLc-2oTVqOH… https://secure-web.cisco.com/16gO9CNWzQHT7IqdPqjexT9AfEDEQl7WrLvpp3Nc_AtMNw… https://secure-web.cisco.com/1gyom5cJyQ8cmW1-ISZiem0NN2me1FWbxC3aS-L8jw2c7m… http://secure-web.cisco.com/11hSSrxQ5y9JDhtiyawoQm5uEXQUx4ke5TYmqszpC-smAH4… https://secure-web.cisco.com/1VUiRWuUGVZcEiJxtLi98il3aVo2D9T3cokDDEuMEzwftN…

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