Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30134 discussions

Fwd: FreeSurfer group analysis visualize data
by Xiuyi Wang 10 Feb '17

10 Feb '17

Hi, I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system. I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis But I got an error message when running this command to visualize uncorrected significance map with freeview. This is the command I typed: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:a nnot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness -age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d I received this error message: Unrecognized sub-option flag ‘annot_outline’ I browsed the internet and found that “That option is only available in the development version of freeview. You can try removing :annot_ouline=1 from the command-line and turn it on manually from the GUI.” So I deleted “:annot_outline=1” and the command line is : freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d But I received another error message: Did not find any volume geometry information in the surface. I found some researchers also have encountered this problem, but it has not been solved. Could you please tell me the solution of the problem? Thank you for your suggestion. Best. Xiuyi Wang

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Re: [Freesurfer] orientation in freeview
by Antonin Skoch 10 Feb '17

10 Feb '17

Dear Zhewei, I think that the problem you report is caused by the fact, that .mat file from FLIRT codes vox2vox transformation, so that cannot be applied to another dataset (in your case fMRI) unless it has the same geometry as the original image the .mat file was generated on. Antonin Can you send your freeview command line and pictures of the mismatch? On 2/9/17 5:58 PM, Zhewei Wang wrote: Hi all, I have a problem maybe relevant to the orientation of images in freeview. I have two images, one is fMRI and one is MRI. They are produced from the same machine at the same time. I loaded both of them in freeview and it showed they are matched very well, even they have different resolutions, different orientation (fMRI is LAS and MRI is PSR), different sform and qform. I registrated MRI to MNI152, and a transformation matrix is generated. I apply this matrix on fMRI, then I got the wrong result: I loaded the fMRI after transformation and MNI152 in freeview, they are not matched. I use /flirt/ for registration. Can anyone explain to me why it happened? At beginning they are shown matched in freeview, even they have different orientation. After apply same transformation, they are shown not matched in freeview even they have same orientation now (both are LAS). Thank you so much. Zhewei

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orientation in freeview
by Zhewei Wang 10 Feb '17

10 Feb '17

Hi all, I have a problem maybe relevant to the orientation of images in freeview. I have two images, one is fMRI and one is MRI. They are produced from the same machine at the same time. I loaded both of them in freeview and it showed they are matched very well, even they have different resolutions, different orientation (fMRI is LAS and MRI is PSR), different sform and qform. I registrated MRI to MNI152, and a transformation matrix is generated. I apply this matrix on fMRI, then I got the wrong result: I loaded the fMRI after transformation and MNI152 in freeview, they are not matched. I use *flirt* for registration. Can anyone explain to me why it happened? At beginning they are shown matched in freeview, even they have different orientation. After apply same transformation, they are shown not matched in freeview even they have same orientation now (both are LAS). Thank you so much. Zhewei

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Re: [Freesurfer] chosen between with and without T2
by X K 10 Feb '17

10 Feb '17

Hi, Very interesting question. But what you found seems to be opposite to previous findings. For example, the figure from a previous paper (Fig. 14 of this paper <http://www.sciencedirect.com/science/article/pii/S1053811913005053>) shows that including T2 data would get thinner (and better) measures. That is, the red line shows the pial surface with only T1 data, while cyan line shows the results based on both T1 and T2. Actually, it is expected that including T2 images would clean some blood vessels and dura close the gray matter. Hope this helps. Xiangzhen

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LGI using Yeo Atlas
by Martin Juneja 10 Feb '17

10 Feb '17

Hi, I used following command to extract LGI values from a set of subjects: recon-all -s <subj> -localGI Output stats is saved in lh.aparc_lgi.stats file. By default, its calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I am interested in calculating LGI values using Yeo atlas of 7 networks. I was wondering how can I change the default atlas to Yeo atlas to get LGI value for each subject. Thanks a lot.

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recon-all -hippocampal-subfields-T1 & matlab version
by X K 10 Feb '17

10 Feb '17

Hi, I'm working with the new version freesurfer 6.0. I found that recon-all with -hippocampal-subfields-T1 could not work well on my system. It reported that matlab 2012b cannot be found (Please see the attached for the error reported. ). I have matlab 2013a and 2016a installed. But it seems that matlab 2012b is needed for running -hippocampal-subfields analysis. Anyone knows how to fix this issue? Or I have to install some matlab 2012b stuffs? Thanks. Best, Xiangzhen -- ----------------------------------------------------------------------------------------- Kong Xiangzhen State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China, 100875.

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chosen between with and without T2
by 巍魏 10 Feb '17

10 Feb '17

Dear FS experts: we use both 6.0 ran a subjects with and without T2 scan，both T1 and T2 are 1x1x1mm，while T1 has 186 scans and T2 has 180，follow pictures showed our results，red line stand with-T2 and green line stand without-T2，obviously red line is more smooth and the grey matter is thicker，but some fellows think red line（with-T2） is not very good at distinguishing the sulcs，we realy want to get your advise about which protocal we should choose [cid:_Foxmail.1@8e2aec7c-df8f-e762-37f5-0a599fadbab2][cid:_Foxmail.1@6edced25-095a-013d-e2eb-ffefca29feda][cid:_Foxmail.1@c394dc84-e072-e21d-cc61-afa638089616][cid:_Foxmail.1@8775cc99-c6df-fa0f-bfe7-a9f7b3d974bb][cid:_Foxmail.1@647ae963-522a-2b78-a232-d7f48537365d][cid:_Foxmail.1@f3c61ee0-94f7-676a-3948-30f90bb26d62][cid:_Foxmail.1@952ee058-cd5d-9d61-b714-c5e523077448][cid:_Foxmail.1@c4c6108a-2b44-e367-9aed-8a273a9be693][cid:_Foxmail.1@5d4e9836-3333-ea45-21a4-43ff1edbb98c][cid:_Foxmail.1@25c7948e-31fb-e4ba-804e-0f7e65dbd4f3][cid:_Foxmail.1@a23af9dc-b3d2-a7db-601e-25a8fab5d6f4][cid:_Foxmail.1@aa5ba067-771c-a6aa-357e-101b7909a9bc][cid:_Foxmail.1@d8f3ddc8-05c5-03b6-fc4a-3b5002ca951d][cid:_Foxmail.1@c87ba4eb-f84f-eeb4-2082-8809e5034ab7][cid:_Foxmail.1@9be2788b-8c20-61f5-718c-2c2a0ec44545][cid:_Foxmail.1@ee10ce20-1842-83d4-2144-66e633d90bc7][cid:_Foxmail.1@ada7aa3c-8759-36c0-0ba0-8916065c4727][cid:_Foxmail.1@4fb3bb63-077e-3559-eeac-7985fcef29b2][cid:_Foxmail.1@620b2133-6071-0819-5689-4c07dc775f98][cid:_Foxmail.1@bf8d70d2-1698-450e-2c71-d5c47043ddd7][cid:_Foxmail.1@153bd520-ff56-8441-f255-f19cd4fa4764][cid:_Foxmail.1@b91948e7-2d3c-af14-4285-82c1aad768e8][cid:_Foxmail.1@595a8609-2191-28d5-f1fa-401a0dd759bd][cid:_Foxmail.1@88a3acfd-dcbf-be88-5ecc-ea84bbc8978c][cid:_Foxmail.1@ba245417-88af-c66b-30a4-619a94d96679] ________________________________ weiqi77777(a)live.com

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Hippocampal subfield segmentation "error" with T1 image
by Gustav Mårtensson 10 Feb '17

10 Feb '17

Hi, I'm planning to run hippocampal subfield segmentation in FreeSurfer 6.0. I have already run the recon-all -all pipeline and are running recon-all -s bert -hippocampal-subfields-T1 as described in https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields . The output, as far as I can see, looks fine but in the very end of hippocampal-subfields-T1.log I get mri_convert.bin discreteLabels.mgz discreteLabelsResampledT1.mgz -rt nearest -odt float -rl /home/gustav/Desktop/preprocessing_h70/bert/mri/norm.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from discreteLabels.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) reading template info from volume /home/gustav/Desktop/preprocessing_h70/bert/mri/norm.mgz... Reslicing using nearest writing to discreteLabelsResampledT1.mgz... mv: cannot stat 'volumesAmygdala.txt': No such file or directory Everything done! It took 1305.6951 seconds Does anyone know what this error ("mv: cannot stat 'volumesAmygdala.txt': No such file or directory") means and if it is of any importance? We are planning on run this command on a few thousand images and we are curious to know this to avoid the risk of re-running everything. We are running on Ubuntu 16.04 LTS with FS version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I've included recon-all.log and hippocampal-subfields-T1.log in case it is of interest. Thank you for your help! -- Gustav Mårtensson | PhD student Division of Clinical Geriatrics Department of Neurobiology, Care Sciences and Society Karolinska Institutet Novum plan 5, 114 57 Huddinge Phone: +46-703-087614 E-mail: gustav.martensson(a)ki.se<mailto:gustav.martensson@ki.se> | ki.se ___________________________________ Karolinska Institutet – a medical university

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recon-all -localGI with longitudinal pipeline output
by Mihaela Stefan 09 Feb '17

09 Feb '17

Hello FreeSurfers, I am trying to run recon-all -s <subjID> -localGI on a longitudinal dataset but I get this error: ERROR: Are you trying to run or re-run a longitudinal time point? If so, please specify the following parameters: \' -long <tpNid> <templateid> \' where <tpNid> is the time point id (SAME as cross sectional ID) and <templateid> is the ID created in the -base run. The directory <tpNid>.long.<templateid> will be created automatically or used for output, if it already exists. Do I really need these if I want to run -localGI or for some reason recon-all thinks that I am trying to re-run the longitudinal pipeline? I renamed the folder replacing "long" (e.g. *OAS2_0001_MR1.new.OAS2_0001 instead of **OAS2_0001_MR1.long.OAS2_0001* ) and recon-all -localGI seems to work. Is there a better way to do this? Thanks! Mihaela

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Topup before trac-all
by Knut J Bjuland 09 Feb '17

09 Feb '17

Hi, I would like to preprocess my dti data with topup (from FSL) before running trac-all. Is this a sensible approach? When I tried running trac-all -prep with the output file from topup (*_hifi_nodif.nii.gz) I got an error message: mv -f /usit/abel/<....>/topuop/146/dmri/bvecs /usit/abel/<...>/topuop/146/dmri/bvecs.norot xfmrot /usit/abel/<...>/topuop/146/dmri/dwi.ecclog /usit/abel/<...>topuop/146/dmri/bvecs.norot /usit/abel/<...>/topuop/146/dmri/bvecs R: Subscript out of range. It seems that there's a problem with bvecs and bvals. Should I reorganise my bvec and bvals? Thank you! Knut J Bjuland

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