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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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How to get the difference between motion, NU intensity correction images and the originate image?
by chen 11 May '19

11 May '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. According to my results, there exsit difference between ROIs. So, i want to check the difference between the originate image and the images after motion and NU intensity correction to confirm the most variation area. How can i get this information?I am looking forward to your kind suggestions.Best regards,Jiachen ------------------

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7T submillimeter resolution processing
by Zeng,Victor (BIDMC - Psychiatry) 10 May '19

10 May '19

Hi all, I have a 7T dataset that I would like to have assistance in running FS6.0 for, and I have used this page as a reference: https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon I have some questions about the recon-all command, namely what the $IMAGE variable actually means. Also I have the $EXPERT_FILE as a txt file that just says: mris_inflate -n 100?. That is fine as well, right? Also I would like to know if the hippocampal/amyg nuc subfield parcellations is designed for 7T usage (In our neuroimaging lab, we've been using it for both 1.5T and 3T). Thanks for your help. Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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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 10 May '19

10 May '19

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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apply m3z warp to list of coordinates
by Benjamin Wittevrongel 10 May '19

10 May '19

External Email - Use Caution Dear, As part of our invasive work, we would like to extract the mni coordinates of intracranial electrodes. To this end, we follow the following procedure: 1) Pre-implant MRI and Post-implant CT are coregistered using SPM. 2) The pre-implant MRI is processed using the recon-all function. 3) The CT is conformed to the 256^3 space, using 'mri_convert ct.nii ctConformed.nii --conform --nochange' 4) The coordinates (in mri-space, i.e. row-column-slice) of the intracranial electrodes are extracted using a custom semi-automated Matlab script. 5) When recon-all finished, the subject is being warped to MNI space, using 'mri_cvs_register --mov subjectId --mni' The last step returns the non-linear warp in an m3z-file. I now want to apply this transformation to the coordinates of the electrodes. For this, I load the m3z-file in matlab, using the 'mris_read_m3z.m' provided by the freesurfer development repository, which gives me two 4-dimensional matrices (256 x 256 x 256 x 3): vol-orig and vol-dest. However, I cannot find any documentation how to interpret these matrices. Could you provide any information on how I would interpret these matrices, and how to apply the warp to the list of CT coordinates (in row-column-slice) to obtain their mni coordinates? Thank you in advance. Best regards, Benjamin Wittevrongel Laboratory for Neuro- and Psychophysiology KU Leuven

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