Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

Help to create flattened images of a whole hemisphere
by Ornaith O Reilly 23 Oct '20

23 Oct '20

External Email - Use Caution Hello Freesurfer developers, I am new to Freesurfer and I'm hoping that someone can help me; I'm attempting to get a flattened patch of an entire hemisphere. Below is a page outlining how to use mris_flatten to achieve this: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch I am just trying to achieve this with the tutorial data to start with. 1. First problem is that when I run the command 'tksurferfv bert lh inflated'; I am getting the error outlined in Image 1. 2. I realised that I could create a patch using freeview instead of tksurfer. However I attempted to follow the instructions on the page above to do this and ran into some problems. Image 2 shows an example of the patch that I created and image 3 shows the error that I get when I attempt to press the Press Fill Uncut Area button (I tried this many times and got the same result). 3. However one time I did succeed in making a patch (I don't know what I did differently this time?) - see image 4 attached. I saved it as lh.full.patch.3d. When I tried to run the command mris_flatten : mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d I got the output: Ornaiths-MacBook-Air-3:surf ornaithoreilly$ mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d using write iterations = 10 reading new surface format patch lh.full.patch.3d with 125717 vertices (94.1% of total) reading original vertex positions... minimizing metric distortion induced by projection... MRISunfold() max_passes = 1 ------- tol=2.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=2, l_nlarea=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 12 niterations 40 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 -------------------- /Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:9034 Error opening parms.fp using filename lh.full.flat.patch.3d.out mode w The version of Freesurfer and the platform that I'm using is outlined below: 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 2) Platform: macOS High Sierra 10.13.6 (17G7024) If anyone could shed some light on any of these errors or suggest an alternative method it would be greatly appreciated. Thanks a lot. Kind Regards

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pial reconstruction with flairSPACE flag
by Octavian Lie 23 Oct '20

23 Oct '20

External Email - Use Caution Dear All, I have downloaded the latest stable (7.1.1), and ran recon-all with and without a high-quality FLAIR SPACE sequence (per Andre's protocols). I noted a new behavior compared with previous FS versions: using the FLAIR makes the pial reconstruction more conservative (blue contour in attached), looks eroded compared with the run without (red contour), the latter which follows the pial anatomy closer (still, it needs some editing out dura at times). I am not sure why that is, I am not sure it is registration per se (the blue pial surface is burrowed within the red one on all sides). Please advise, is there a way to 'relax' the recons with FLAIR SPACE to overlap better with the actual pial surface? Thank you, Octavian

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Help to create flattened images of a whole hemisphere
by Ornaith O Reilly 23 Oct '20

23 Oct '20

External Email - Use Caution Hello Freesurfer developers, I am new to Freesurfer and I'm hoping that someone can help me; I'm attempting to get a flattened patch of an entire hemisphere. Below is a page outlining how to use mris_flatten to achieve this: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch I am just trying to achieve this with the tutorial data to start with. 1. First problem is that when I run the command 'tksurferfv bert lh inflated'; I am getting the error outlined below: Ornaiths-MacBook-Air-3:subjects ornaithoreilly$ tksurferfv bert lh inflated freeview -f /Applications/freesurfer/7.1.1/subjects/bert/surf/lh.inflated:curvature=/Applications/freesurfer/7.1.1/subjects/bert/surf/lh.curv -viewport 3d /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then' Ornaiths-MacBook-Air-3:subjects ornaithoreilly$ 2. I realised that I could create a patch using freeview instead of tksurfer. However I attempted to follow the instructions on the page above to do this and ran into some problems. Image 2 shows an example of the patch that I created but when I attempt to press the Press Fill Uncut Area button (I tried this many times and got the same result) a pop up appeared saying "please move cursor to a valid vertex". 3. However one time I did succeed in making a patch (I don't know what I did differently this time?) - see image 4 attached. I saved it as lh.full.patch.3d. When I tried to run the command mris_flatten : mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d I got the output: Ornaiths-MacBook-Air-3:surf ornaithoreilly$ mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d using write iterations = 10 reading new surface format patch lh.full.patch.3d with 125717 vertices (94.1% of total) reading original vertex positions... minimizing metric distortion induced by projection... MRISunfold() max_passes = 1 ------- tol=2.0e-01, sigma=0.0, host=unkno, nav=1024, nbrs=2, l_nlarea=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 12 niterations 40 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 -------------------- /Users/developer/space_freesurfer/build/tulum/trunk/developer-7.1.1/utils/mrisurf_metricProperties.cpp:9034 Error opening parms.fp using filename lh.full.flat.patch.3d.out mode w The version of Freesurfer and the platform that I'm using is outlined below: 1) FreeSurfer version: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 2) Platform: macOS High Sierra 10.13.6 (17G7024) If anyone could shed some light on any of these errors or suggest an alternative method it would be greatly appreciated. Thanks a lot. Kind Regards Ornaith O'Reilly

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please help me
by saman fouladi 23 Oct '20

23 Oct '20

External Email - Use Caution hi How long does it take to execute a recon-all command? and what message indicates that it finished? Is there a way to speed it up? thank you

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The non-existent field'numEntries' is referenced.(write_annotation.m)
by 1248742467 22 Oct '20

22 Oct '20

External Email - Use Caution hello, fs when i use the write_annotation.m, the error message occurs: `The non-existent field'numEntries' is referenced. Error write_annotation (line 62) count = fwrite(fp, int32(ct.numEntries),'int'); Error test_1 (line 13) write_annotation('rh.aparc.a2009s.annot', c, b, ct)` How to solve the non-existent field'numEntries' is referenced？By the way, can ct change automatically according to the value of label?

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longitudinal study
by KennethSPrice 22 Oct '20

22 Oct '20

External Email - Use Caution Hello, I am running a longitudinal study and am examining the pial surface for my 2 timepoints. The surfaces are slightly offset. Will this effect my statistical analysis for volume and thickness? I have attached the pial surface for each time point to this email. Should I be examining timpoint1.long and timepoint2.long instead? Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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lta files longitudinal pipeline
by Marisa Johanna Nordt 22 Oct '20

22 Oct '20

External Email - Use Caution Hi, I have a question about the lta files from the longitudinal pipeline (using the –affine flag). Instead of just one .lta file from each timepoint to the template 3 different .lta files are saved -tp1_to_templ_norm.lta, -tp1_to_templ_affine.lta, -tp1_to_templ.lta Is the one created last (tp1_to_templ.lta) the final lta-file that I can use to align additional files from tp 1 to the template? Thanks a lot! Marisa

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Re: [Freesurfer] Question: Longitudinal Edits
by Martin Reuter 22 Oct '20

22 Oct '20

Hi Suzan, (sending this also to the FS support list, where these questions fit best, but sometimes I miss emails there). If edits are necessary or not depends purely on the quality of your data. I.e. old scanners, low contrast, motion artefacts etc. It also depends on the number of subjects. If you want to quantify small changes in only a few subjects, you need to make sure that FS results are clean and correct. If you are running a population study with 30.000 people you cannot do manual edits at all and have to resort to a quality control paradigm. Furthermore, the longitudinal stream additionally benefits from having the subject template (aka “base”). Usually it is sufficient to edit that instead of all time points (e.g. for skullstrip or surface related problems). In short FreeSurfer does not require edits, it allows users to include edits if they like. It is recommended to check results. Never trust any automated tool blindly. Best, Martin > On 22. Oct 2020, at 03:46, Suzan Maleki <suzan.maleki(a)monash.edu> wrote: > > > Dear Martin, > > The time and effort of the FreeSurfer team is really appreciated. I would be grateful if you explain to what extent it is necessary to apply manual edits for longitudinal processing ? > I have read the FS longitudinal tutorial and noticed so many manual edits need to be done on Cross > Base >Long scans. For example, having two time-points that are 3 months apart, is it really necessary to do manual edits for all the individuals ? > I am wondering what are the reasons that necessitate several manual edits for longitudinal pipeline, considering that FreeSurfer is one of the best available and commonly used neuroimaging softwares and supposed to be fully automated. > Also, how much those manual edits will affect the reproducibility of the processing ? > Thanks a lot for your help, > Kind regards, > Suzan > > -- > Suzan Maleki > PhD Student > > <>Brain, Mind and Society Research Hub > Turner Institute for Brain and Mental Health > School of Psychological Sciences > Monash University > 770 Blackburn Road > Clayton VIC 3800 Australia > > E: suzan.maleki(a)monash.edu <mailto:suzan.maleki@monash.edu> > W: www.brainmindsociety.com <http://www.brainmindsociety.com/>

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unpacksdcmdir in version 7: issues with cfg files
by Caspar M. Schwiedrzik 22 Oct '20

22 Oct '20

External Email - Use Caution Hi! We are encountering some issues with unpacksdcmdir in version 7.1.1. In particular, it turns out that the handling of cfg files seems to have changed, which makes things somewhat impractical. Old (v5.3) cfg files cannot be used anymore, because only dicom series names that are actually present in the current session are accepted. This makes it impossible to have one general cfg file for different experiments, and also to help structure the cfg files with commented lines. I understand unpacksdcmdir is being phased out, but the flexibility brought about by cfg files still makes this a very handy tool. Yet, the current version has lost much of this flexibility. I suggest reverting to the way unpacksdcmdir handled cfg files in the past. Thanks, Caspar

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Infant FreeSurfer issues
by k3ops＠free.fr 22 Oct '20

22 Oct '20

External Email - Use Caution Hi FreeSurfer team, I’ve been using the Infant FreeSurfer pipeline on 3DT1 sequences for few weeks now on infants from 0.4 to 5.4 years-old. I know Infant FreeSurfer is recommended for 0-2 years old infant but standard FreeSurfer was failing due to many lacunar infarcts in the white matter. So I tried Infant FreeSurfer with an age of 2 years old even for 2 to 5.4 years-old subjects and results look good. I know standard FreeSurfer has been tested on infant from 4.2 years-old, so what would be your recommendation for subjects from 2 to 4.2 years old? Have you already run Infant FreeSurfer on subjects older than 2 years-old? Do you recommend it? I also have some processing issues with my actual data: 1. Pixels with 0 value => probably out of the brainmask so the pixels are set to 0 after masking So, sometimes lateral ventricles are miss-segmented (https://ibb.co/JpWG9st) 2. Thalamus region is missing from the aseg stat export (always equal to 0 mm3), do you have a fix? Should I fix a LUT file? 3. Would it be possible to get the non-skullstripped N3 corrected 3D T1 in the MNI space (3D iso)? I was not able to find the registered 3DT1 to re-apply the N3 correction, I only found the input 3DT1 (mprage.nii.gz) in its native space. 4. Do you have any workaround for large ventricles segmentation issue (https://ibb.co/nnbZcYs)? Standard FreeSurfer has a -bigventricle option, do you have a similar approach? And some additional questions: • brainstem seems to be split into multiple sub-regions, is it possible get the entire brainstem volume in the aseg stat export? • I saw that corpus callosum is not present in the “aseg” segmentation, so is this region out of the Infant FreeSurfer atlases? • Is it possible to get the mean cortical thickness for the labels you are providing? Many thanks as I know there are plenty of questions here :) Best, Florent

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Freesurfer October 2020