Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

Longitudinal processing
by falk.luesebrink＠med.ovgu.de 13 May '19

13 May '19

External Email - Use Caution Dear all, I'm a beginner in using the longitudinal processing pipeline (as well as statistical analysis) and it would be great to get some insights or hints to analyze my data. I have a dataset consisting of 11 subjects each acquired at 7 different time points with an isotropic resolution of 1 and 0.8 mm at 3T using a 64-channel head coil. Using that dataset I want to investigate short term differences in e.g. cortical thickness with the goal to assess the degree of biological variance during that time period. I have plotted the mean cortical thickness of each time point of every subject (using lme_timePlot and lme_lowessPlot) showing a somewhat random distribution across time and from my perspective fairly high standard deviation. I wanted to have a look at the individual percent change by overlaying the symmetric percent change on fsaverage, but wasn't quite sure of the scale. Is it in percent? So in case I set the scale bar between 1 and 5, the color relates to 1 to 5 percent? What other ways would make sense to have a look at? I definitely cannot compare groups, as there is just one. The days and time of acquistion are rather randomly choosen, so I potentially cannot use either as a covariate. Best, Falk ............................................... [klinikum_logo_schmal_e-mail_blau] University Clinic for Neurology Otto-von-Guericke-university Magdeburg Medical faculty Leipziger Str. 44 39120 Magdeburg Phone +49-391-6117-512 falk.luesebrink(a)med.ovgu.de<mailto:falk.luesebrink@med.ovgu.de> http://www.kneu.ovgu.de/kneu.html

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Longitudinal Gray/white Contrast Measure
by WON JONG CHWA 13 May '19

13 May '19

External Email - Use Caution Dear FreeSurfer experts, I am currently running a longitudinal analysis in FreeSurfer v5.3 to look at changes in volume and gray/white contrast. I ran all the processing steps and used this command below to look at results for volume: long_mris_slopes --qdec ./qdec/qdec.table.dat --meas volume --hemi lh --do-label --do-rate --time years --qcache fsaverage --sd $SUBJECTS_DIR We also would like to look at change in gray-white matter intensity ratio over time (between 2 timepoints) as well, but there is no separate measure defined for it. I was wondering what we can do to calculate this. Thank you. William

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How to get the difference between motion, NU
by chen 13 May '19

13 May '19

External Email - Use Caution Hi expert, I selected hippocampus and amygdala as ROIs to estimated the reliability of a well-controlled multi-site study. The travelling volunteers were scanned in each site with the same type scanners and scan protocol. But, amygdala volume (generated by FreeSurfer) presented a relatively poor ICC scores between sites. So, i want to found the reasons from sites or scanners. According to previous studies, the variation might come from across-site difference and the structure itself. And the major sources of between-site variation might be related to field inhomogeneity and other issues idiosyncratic to individual each scanners. Due to this reason, i want to check my data to confirm the field inhomogeneity located in amydala area or not. How can i get the difference between the originate image and the images after motion and NU intensity? I am looking forward to your suggests. Cheers, Jiachen

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recon-all errors at Talairach
by QN Z 12 May '19

12 May '19

External Email - Use Caution Dear Experts, I got recon-all errors at Talairach both on my own data and sample file (nii.gz) converted from the FreeSurfer installation tutorial. I reinstalled my platform and FreeSurfer 5.3.0 a few days ago, however the errors still exited. My code is as follows: export SUBJECTS_DIR=/home/zqn/freesurfer/subject recon-all -s ST_LS_004 -i /home/zqn/freesurfer/subjects/ST_LS_004.nii recon-all -s ST_LS_004 -all The errors appeared after the third command line was input and the errors are as follows: #-------------------------------------------- #@# Talairach 2019年 05月 13日星期一 10:11:56 CST /home/zqn/freesurfer/subjects/ST_LS_004/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux zqn-Precision-Tower-3620 4.18.0-18-generic #19~18.04.1-Ubuntu SMP Fri Apr 5 10:22:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ST_LS_004 exited with ERRORS at 2019年 05月 13日星期一 10:11:57 CST ----------------------------------------------- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Platform: Ubuntu 18.04 recon-all.log: see attached file I am brand new to FreeSurfer and I read the recon-all.log but could not find out what the errors exactly are and the way to solve it. Any reply or suggestion is highly appreciated. Thank you so much! Qiannan Zhao

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Re: [Freesurfer] A Question about How to Map Parcels of the Cortex on the surface of the Brain Cortex
by Bruce Fischl 12 May '19

12 May '19

Hi Mahshid you can't sample cerebellar or brainstem labels onto the cortical surface as it only represents cerebral cortex. You could create tessellations for either of them using mri_mc or mri_tessellate. You can sample your cortical labels to surface-based label files using mri_vol2label or to annotations using mris_sample_parc. cheers Bruce On Sun, 12 May 2019, Mahshid Fouladivanda wrote: > > External Email - Use Caution > > > Hi, > > Thanks again, for your helpful reply. The parcellation file is .nii (not extracted from Freesurfer > but in T1 space) and the surface is .pial (extracted from free surfer). > By the way, the parcellation included cerebellum and brain stem which there are not in the output > of the Freesurfer surfaces! Is it possible to keep up the cerebellum and brain stem while creating > pial surface in Freesurfer? > Thanks a lot. > > Regards, > Mahshid > > > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Mahshid Fouladivanda <M.Fouladivanda(a)sutech.ac.ir> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu>, DGREVE(a)mgh.harvard.edu > Date: Sat, 11 May 2019 14:47:48 -0400 (EDT) > Subject: Re: [Freesurfer] A Question about How to Map Parcels of the Cortex on the surface of > the Brain Cortex > Hi Mashid > > We don't resample to a template space. Everything is in one native > coordinate system or another (not quite the original scanner coords, but > close). You can register based on just the image header, but without > knowing more about your data and what format it is stored in I don't > think we can help > > cheers > Bruce > On Sat, 11 May 2019, Mahshid Fouladivanda wrote: > > > > > External Email - Use Caution > > > > Dear Prof. Fichl and Prof. Douglas > > > > Thanks for your replay. > > By the way, My parcels have not been extracted from Freesurfer by using "recon-all". While, the > > command "mri_vol2surf" needs registration file as input. Still, is it possible to use the > mentioned > > command?? If yes, so what about the registration information? I think that registration file > > extracted from tkregister or etc, is for registering the output of the recon-all between the > native > > space and Freesurfer template space. However, my parcels are not from Freesurfer. I don't know > > maybe I think wrong! I would be grateful by receiving your help. > > > > Regards, > > Mashid > > > > Date: Fri, 10 May 2019 18:58:40 +0000 > > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > > Subject: Re: [Freesurfer] A Question about How to Map Parcels of the > > Cortex on the surface of the Brain Cortex > > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > Message-ID: <d2312cef-2e80-2690-501e-83895bd26dad(a)mgh.harvard.edu> > > Content-Type: text/plain; charset="utf-8" > > > > Are the parcels in the volume or on the surface? If in the volume, then use mri_vol2surf to map > > them (as a "segmentation") onto the surface, then use mris_seg2annot to create an annotation > file. > > Run either with --help to get docs and examples > > > > On 5/10/2019 2:26 PM, Bruce Fischl wrote: > > Hi Mahsid > > > > matlab is probably the easiest way, but without knowing what format you have them in it isn't > easy > > for us to say. In matlab you can use write_annotation or write_ascii_curv or something to get it > > into a format we can handle > > > > cheers > > Bruce > > > > > > cheers > > Bruce > > On Fri, 10 May 2019, mahshid fouladivand wrote: > > > > > > External Email - Use Caution > > > > Hello Dear Freesurfer Experts, > > > > I have a high resolution brain cortex parcellation that is not extracted from Freesurfer. Now I > > want to display the nodes(each parcels) on the pial and inflated surfaces. Both pial and inflated > > surfaces have been extracted from T1mprage image of the corresponding subject using recon-all. > > Also, the parcels and the T1 image are in the same space. Now, I am wondering is it possible to > map > > these parcels on the Freesurfer pial/inflated surface? > > By the way, How can I create an .annot file for my parcels? > > If you could help me with this, I really appreciate your help. > > > > Regards, > > Mahshid > > > > > > > > > >

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recon-all exited ERRORS
by QN Z 12 May '19

12 May '19

External Email - Use Caution Hello FreeSurfer Developers, I am a student learning FreeSurfer and attempting to compute cortical volume and other brain structural measurements for my subjects. So I ran recon-all on several subjects and the sample subjects converted from FreeSurfer installation tutorial. The first step for recon-all did not exit with errors (command line: recon-all -s sample-001 -i /home/zqn/freesurfer/subjects/sample-001.nii.gz). But I got the following error when I ran the second step for recon-all (command line: recon-all -s sample-001 -all): recon-all -s sample-001 exited with ERRORS I cannot find out what the error is and the way to solve it. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Ubuntu 18.04 3) recon-all.log: see attached Hope to hear from you soon. Thanks, Sincerely, Qiannan

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Atlas Labelling on Registered images
by Bunting, Emma 12 May '19

12 May '19

External Email - Use Caution Hi Freesurfer experts, Does reconall register each T1 to fsaverage space? And if yes, are the Desikan-Killany and Destrieux atlas labels still applicable? I am asking because I noticed that when I overlayed the Desikan-Killany atlas onto our reconall outputs they didn’t seem to align properly, Thanks, Emma Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Re: [Freesurfer] A Question about How to Map Parcels of the Cortex on the surface of the Brain Cortex
by Mahshid Fouladivanda 11 May '19

11 May '19

External Email - Use Caution Dear Prof. Fichl and Prof. Douglas Thanks for your replay. By the way, My parcels have not been extracted from Freesurfer by using "recon-all". While, the command "mri_vol2surf" needs registration file as input. Still, is it possible to use the mentioned command?? If yes, so what about the registration information? I think that registration file extracted from tkregister or etc, is for registering the output of the recon-all between the native space and Freesurfer template space. However, my parcels are not from Freesurfer. I don't know maybe I think wrong! I would be grateful by receiving your help. Regards, Mashid Date: Fri, 10 May 2019 18:58:40 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] A Question about How to Map Parcels of the Cortex on the surface of the Brain Cortex To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <d2312cef-2e80-2690-501e-83895bd26dad(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Are the parcels in the volume or on the surface? If in the volume, then use mri_vol2surf to map them (as a "segmentation") onto the surface, then use mris_seg2annot to create an annotation file. Run either with --help to get docs and examples On 5/10/2019 2:26 PM, Bruce Fischl wrote: Hi Mahsid matlab is probably the easiest way, but without knowing what format you have them in it isn't easy for us to say. In matlab you can use write_annotation or write_ascii_curv or something to get it into a format we can handle cheers Bruce cheers Bruce On Fri, 10 May 2019, mahshid fouladivand wrote: External Email - Use Caution Hello Dear Freesurfer Experts, I have a high resolution brain cortex parcellation that is not extracted from Freesurfer. Now I want to display the nodes(each parcels) on the pial and inflated surfaces. Both pial and inflated surfaces have been extracted from T1mprage image of the corresponding subject using recon-all. Also, the parcels and the T1 image are in the same space. Now, I am wondering is it possible to map these parcels on the Freesurfer pial/inflated surface? By the way, How can I create an .annot file for my parcels? If you could help me with this, I really appreciate your help. Regards, Mahshid

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Re: [Freesurfer] Cortical Thickness Extraction
by Bunting, Emma 11 May '19

11 May '19

External Email - Use Caution Hi Doug, Why should we not scale the thickness by the ICV? This is what we had thought to be the norm based on the literature, How would you advise normalising these values instead? Best wishes, Emma Greve, Douglas N.,Ph.D.<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 18 Mar 2019 07:56:18 -0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> They do not have any normalization applied. BTW, you should not scale the thickness by the ICV On 3/18/19 10:24 AM, Bunting, Emma wrote: External Email - Use Caution Hi Freesurfer experts, I used a script created by ENIGMA to extract the cortical thickness values for 129 subjects that had undergone reconall processing. We are using these values in VBM analysis. From reading other papers, we notice that all regional volumes are usually normalised by dividing by total intracranial volumes for each subject. I’m just wondering whether the values we are extracting from our freesurfer output files have already had this normalisation applied? The script we’ve used as follows: #!/bin/bash echo 'SubjID,L_bankssts_thickavg,L_caudalanteriorcingulate_thickavg,L_caudalmiddlefrontal_thickavg,L_cuneus_thickavg,L_entorhinal_thickavg,L_fusiform_thickavg,L_inferiorparietal_thickavg,L_inferiortemporal_thickavg,L_isthmuscingulate_thickavg,L_lateraloccipital_thickavg,L_lateralorbitofrontal_thickavg,L_lingual_thickavg,L_medialorbitofrontal_thickavg,L_middletemporal_thickavg,L_parahippocampal_thickavg,L_paracentral_thickavg,L_parsopercularis_thickavg,L_parsorbitalis_thickavg,L_parstriangularis_thickavg,L_pericalcarine_thickavg,L_postcentral_thickavg,L_posteriorcingulate_thickavg,L_precentral_thickavg,L_precuneus_thickavg,L_rostralanteriorcingulate_thickavg,L_rostralmiddlefrontal_thickavg,L_superiorfrontal_thickavg,L_superiorparietal_thickavg,L_superiortemporal_thickavg,L_supramarginal_thickavg,L_frontalpole_thickavg,L_temporalpole_thickavg,L_transversetemporal_thickavg,L_insula_thickavg,R_bankssts_thickavg,R_caudalanteriorcingulate_thickavg,R_caudalmiddlefrontal_thickavg,R_cuneus_thickavg,R_entorhinal_thickavg,R_fusiform_thickavg,R_inferiorparietal_thickavg,R_inferiortemporal_thickavg,R_isthmuscingulate_thickavg,R_lateraloccipital_thickavg,R_lateralorbitofrontal_thickavg,R_lingual_thickavg,R_medialorbitofrontal_thickavg,R_middletemporal_thickavg,R_parahippocampal_thickavg,R_paracentral_thickavg,R_parsopercularis_thickavg,R_parsorbitalis_thickavg,R_parstriangularis_thickavg,R_pericalcarine_thickavg,R_postcentral_thickavg,R_posteriorcingulate_thickavg,R_precentral_thickavg,R_precuneus_thickavg,R_rostralanteriorcingulate_thickavg,R_rostralmiddlefrontal_thickavg,R_superiorfrontal_thickavg,R_superiorparietal_thickavg,R_superiortemporal_thickavg,R_supramarginal_thickavg,R_frontalpole_thickavg,R_temporalpole_thickavg,R_transversetemporal_thickavg,R_insula_thickavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV' > CorticalMeasuresENIGMA_ThickAvg.csv echo 'SubjID,L_bankssts_surfavg,L_caudalanteriorcingulate_surfavg,L_caudalmiddlefrontal_surfavg,L_cuneus_surfavg,L_entorhinal_surfavg,L_fusiform_surfavg,L_inferiorparietal_surfavg,L_inferiortemporal_surfavg,L_isthmuscingulate_surfavg,L_lateraloccipital_surfavg,L_lateralorbitofrontal_surfavg,L_lingual_surfavg,L_medialorbitofrontal_surfavg,L_middletemporal_surfavg,L_parahippocampal_surfavg,L_paracentral_surfavg,L_parsopercularis_surfavg,L_parsorbitalis_surfavg,L_parstriangularis_surfavg,L_pericalcarine_surfavg,L_postcentral_surfavg,L_posteriorcingulate_surfavg,L_precentral_surfavg,L_precuneus_surfavg,L_rostralanteriorcingulate_surfavg,L_rostralmiddlefrontal_surfavg,L_superiorfrontal_surfavg,L_superiorparietal_surfavg,L_superiortemporal_surfavg,L_supramarginal_surfavg,L_frontalpole_surfavg,L_temporalpole_surfavg,L_transversetemporal_surfavg,L_insula_surfavg,R_bankssts_surfavg,R_caudalanteriorcingulate_surfavg,R_caudalmiddlefrontal_surfavg,R_cuneus_surfavg,R_entorhinal_surfavg,R_fusiform_surfavg,R_inferiorparietal_surfavg,R_inferiortemporal_surfavg,R_isthmuscingulate_surfavg,R_lateraloccipital_surfavg,R_lateralorbitofrontal_surfavg,R_lingual_surfavg,R_medialorbitofrontal_surfavg,R_middletemporal_surfavg,R_parahippocampal_surfavg,R_paracentral_surfavg,R_parsopercularis_surfavg,R_parsorbitalis_surfavg,R_parstriangularis_surfavg,R_pericalcarine_surfavg,R_postcentral_surfavg,R_posteriorcingulate_surfavg,R_precentral_surfavg,R_precuneus_surfavg,R_rostralanteriorcingulate_surfavg,R_rostralmiddlefrontal_surfavg,R_superiorfrontal_surfavg,R_superiorparietal_surfavg,R_superiortemporal_surfavg,R_supramarginal_surfavg,R_frontalpole_surfavg,R_temporalpole_surfavg,R_transversetemporal_surfavg,R_insula_surfavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV' > CorticalMeasuresENIGMA_SurfAvg.csv for subj_id in $(ls -d Subj*); do #may need to change this so that it selects subjects with FS output printf "%s," "${subj_id}" >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%s," "${subj_id}" >> CorticalMeasuresENIGMA_SurfAvg.csv for side in lh.aparc.stats rh.aparc.stats; do for x in bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula; do printf "%g," `grep -w ${x} ${subj_id}/stats/${side} | awk '{print $5}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `grep -w ${x} ${subj_id}/stats/${side} | awk '{print $3}'` >> CorticalMeasuresENIGMA_SurfAvg.csv done done printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g" `cat ${subj_id}/stats/aseg.stats | grep IntraCranialVol | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g" `cat ${subj_id}/stats/aseg.stats | grep IntraCranialVol | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv echo "" >> CorticalMeasuresENIGMA_ThickAvg.csv echo "" >> CorticalMeasuresENIGMA_SurfAvg.csv done Please let me know if you need any other info, Best wishes, Emma Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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How Can I Keep up Brain-stem and Cerebellum while Creating .pial and .inflated Surfaces by using "Recon all" Command?
by Mahshid Fouladivanda 11 May '19

11 May '19

External Email - Use Caution Dear Freesurfer Experts, I need a brain cortex surface including Brain-stem and Cerebellum. Using "recon-all" command, Brain-stem and Cerebellum has been removed from the output pial files. How can I set the command in order to keep up Brain-stem and Cerebellum with brain cortex surface? I would appreciated any help. Regards, Mahshid

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Freesurfer May 2019