Re: [Freesurfer] recon all

ely, Zheng At 2021-01-28 23:27:27, "Douglas N. Greve" wrote: No head motion correction because there is only one image On 1/27/2021 6:59 PM, 郑凤莲 wrote: External Email - Use Caution Hi experts, We have segmented hippocampus using Freesurfer 6.0. I hav

[Freesurfer] recon all

External Email - Use Caution Hi experts, We have segmented hippocampus using Freesurfer 6.0. I have a question that is there "head motion correct" in this step? If yes, how does it examined? I am looking forward to your reply. Thanks very much. Sincerely, Zheng | |

[Freesurfer] mgz to nifty {Disarmed}

External Email - Use Caution Hi experts, I am using FS for some studies. Now, I have a question about format convertion. How can I convert .mgz file to .nii file. Is there any way to complete? Thanks for your contention in advance. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0

[Freesurfer] hippocampal subfields {Disarmed}

. Sincerely, Zhemg | | 郑凤莲 | | 邮箱：zhengfenglian0...@163.com | 签名由 网易邮箱大师 定制___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Hippocampal subfields

49:30, "Iglesias Gonzalez, Juan E." wrote: Dear Zheng, Can you please send us the log files? Kind regards, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of 郑凤莲 Reply-To: Fre

[Freesurfer] Hippocampal subfields

External Email - Use Caution Hi exports, I am using FS6.0 to segment hippocampus. I run "recon-all -s bert -hippocampal-subfields-T1" and it said "recon all bert finished without error". However, in mri directory, there is no l(r)h.hippoSfLabels-T1.v10.mgz file. And in tmp dir

[Freesurfer] (无主题) {Disarmed} {Disarmed}

, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0...@163.com | 签名由 网易邮箱大师 定制___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Thalamus segmentation {Disarmed}

x27;t know the reason for this cese. I am looking forward to your reply. Thanks very much in advance. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0...@163.com | 签名由 网易邮箱大师 定制___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Thalamic segmentation

External Email - Use Caution Hi Expert, In the latest version of FS, I have segmented the thalamic successfully. But I can't use Freeview to show the segmentation map. There is an error :"freeview: /usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by /opt/freesurfe

[Freesurfer] Thalamic nuclei segmentation

External Email - Use Caution Hi experts, I have segmented the thalamic nuclei into 25 nuclei using the new FS version. However, when I input "freeview -v nu.mgz -v ThalamicNuclei.v10.T1.mgz:colormap=lut ", there is no 3D atlas in Freeview, just nu.mgz. What's the matter? Please

[Freesurfer] LGI in QDEC

External Email - Use Caution Hi experts, I am using qdec software for the statistic of LGI. I have created the .Qdecrc file. However, when I set Monte Carlo Null-Z Simulation (fwhm=10), there is an error: "Error running mri_surfcluster, Error: fwhm out-of-range(<1 or >30)". Then

[Freesurfer] Thalamic Nuclei {Disarmed}

there another new version for the thalamic? Could you share me the new version? Thanks very much in advance. Look forward to your reply. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0...@163.com | 签名由 网易邮箱大师 定制___ Freesurfer mailing list Frees

[Freesurfer] visual cortex {Disarmed}

, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0...@163.com | 签名由 网易邮箱大师 定制___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] GLM

External Email - Use Caution Hi experts, I am using FS 6.0 for analyzing the cortical thickness difference between 3 groups: patient1, patient2 and control. In DODS model, I need to creat 2 files, FSDG and mtx file. And we have 3 variables: age, gender and cortical thickness.

[Freesurfer] GLM

External Email - Use Caution Dear experts, I am using FS 6.0 for some studies. I want to calculate the thickness difference between males and females in two group, Young group and Old group. In DODS model: The first step: creat a FSDG file: GroupDescriptorFile 2 Title Tutoria

Re: [Freesurfer] Cortical surface

On 8/12/18 5:17 AM, 郑凤莲 wrote: External Email - Use Caution Dear experts, I an using FS 6.0 for cortical reconstructions. I can show whole brain regions (tksurfer...), as shown in the picture. However, I just want to show insular region. Is there any way to complet

[Freesurfer] Cortical surface

External Email - Use Caution Dear experts, I an using FS 6.0 for cortical reconstructions. I can show whole brain regions (tksurfer...), as shown in the picture. However, I just want to show insular region. Is there any way to complete it? I am looking forward to your reply.

[Freesurfer] Hippocampal and amygdala subfields

External Email - Use Caution Hi experts, I am using FS dev version for hippocampal and amygdala subfields. It's an automatic progress. Reviewers suggested that "Was the hippocampal and amygdala segmentation visually inspected?" We have visually inspected the segmentation and the

[Freesurfer] Hypothalamus

. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0...@163.com | 签名由 网易邮箱大师 定制___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to

[Freesurfer] e-mail error {Disarmed}

Hi FS list, When I sent an e-mail to you, I always recieved a disarmed e-mail, as follows: What' wrong? Is there any way to resolve it? Sincerely, Zheng | | 13181786167 邮箱：13181786...@163.com | 签名由 网易邮箱大师 定制___ Freesurfer mailing list Freesurfer@n

[Freesurfer] Recon-all {Disarmed}

Hi experts, I am using FS 6.0 for LGI. My data is fetal images. I ran "recon-all" pipeline for cotical thickness and LGI. Is it suitable? Or are the results reliable, such as the LGI value of precental? I am looking forward to your reply. Thank you very much. Sincerely, Zheng

[Freesurfer] RECON-ALL {Disarmed}

Hi experts, I am using FS 6.0 to calculate LGI. But when l ran recon-all, there is an error: couldn't find DWI parameters. I don't know how to resolve this problem. Looking forward to your reply. Thanks very much. Sincerely, Zheng | | 13181786167 邮箱：13181786...@163.com | 签名由 网易邮箱大师 定制___

[Freesurfer] Hippocampus subfields {Disarmed}

Hi Experts, I ran the segmentation of hippocampus in Freesurfer dev version. The left or right whole volume isn't equal to the sum of 12 subfields. But it is equal to the sum of the volume of tail, whole head and body. Why? I am looking forward to your reply. Thank you very much. Sincerely, Zh

[Freesurfer] Hippocampal subfields {Disarmed}

Hi professors, I ran the segmentation of hippocampus in Freesurfer dev version. The left or right whole volume isn't equal to the sum of 12 subfields. But it is equal to the sum of the volume of tail, whole head and body. Why? I am looking forward to your reply. Thank you very much. Sincerely,

[Freesurfer] dev version

Hi all experts, I am using freesurfer dev version for segmentation of hippocampus and amydala. I have a doubt about it. 1. In FS 6.0, I can type '203-226' in freeview for viewing subfields of hippocampus. In dev version, When I type 'freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v2x.FS60.mgz:c

[Freesurfer] Amydala segmentation

Hi FS experts, I ran "segmentHA_T1.sh 0010006 $SUBJECTS_DIR" for amydala segmentations. But there is only hippocampal subfields, no amydala segmentation .txt file in mri file. I ran ''recon-all'' in FS 6.0, and copy segmentHA_T1.sh and checkMCR to FREESURFER_HOME. Why there is no files

[Freesurfer] GC-DG

Hi professor, I am using FS 6.0 for hippocampal subfield. I have a doubt what is the full name of GC-DG? I didn't find it in the wiki. Sincerely, Zheng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/

Re: [Freesurfer] LGI ERROR

FWHM is a mixture of the applied FWHM and smoothness inherent in the data. LGI has a lot of inherent smoothness, so the final FWHM is very large. The MC sim table only goes up to 30mm, after that it generates an error On 12/13/17 2:19 AM, 郑凤莲 wrote: Hi professors, I am using Freesurf

[Freesurfer] LGI ERROR

Hi professors, I am using Freesurfer 6.0 for calculating LGI. I have done 'recon-all' for it. When I ran Monte Carlo in qdec (FWHM=10), it has errors: However, when FWHM=5, It was ok. What led to this result? I don't know why. Thanks in advance ! Zheng

[Freesurfer] Thalamus and Thalamus-Proper

Hi FS professors, I am using FS 6.0 for subcortical structures. I have a doubt about thalamus and thalamus-Proper. I added thalamus to brainmask.mgz in Freeview, it shows nothing. However, choose thalamus-Proper, it's ok. I just want to ensure whether the thalamus-Proper in Freesurfer i

Re: [Freesurfer] subcortical structures volume

Zheng > >For volume, usually including eTIV reduces the variance and increases power >more than you lose for having one additional regressor. Not sure about >gender - how unbalanced is your sample? You might be ok with just eTIV >Bruce > > >On Sat, 2 Dec 2017, 郑凤莲 >wrote:

Re: [Freesurfer] subcortical structures volume

an by >"which stat analysis". > > >On 12/01/2017 07:50 PM, 郑凤莲 wrote: >> Hi professor, >> >>I am using Freesurfer 6.0 and get the volume of subcortical >> structures. I want to get the relationship between age and volume. I >> only have one group,

Re: [Freesurfer] subcortical structures volume

nly reflect differences in head size > >cheers >Bruce >On Sat, 2 Dec 2017, 郑凤莲 wrote: > >> Hi Bruce, >> >> I think I get it. I have 27 males and 28 females and 26 males. It isn't >> necessary to corrected by eTIV. Is it right? >> >> Th

Re: [Freesurfer] subcortical structures volume

e variance and increases power >more than you lose for having one additional regressor. Not sure about >gender - how unbalanced is your sample? You might be ok with just eTIV >Bruce > > >On Sat, 2 Dec 2017, 郑凤莲 >wrote: > >> Hi professor, >> >>I am us

[Freesurfer] subcortical structures volume

Hi professor, I am using Freesurfer 6.0 and get the volume of subcortical structures. I want to get the relationship between age and volume. I only have one group, is it necessary to take gender and eTIV as a covariate? If it is necessary, Which statistical analysis should be used? I rea

Re: [Freesurfer]  hippocampus subfields

what should I do? The picture is my result, but it doesn't corrected by eTIV. I appreciate your help, please. Thanks a lot! Zheng At 2017-11-22 10:29:43, "Bruce Fischl" wrote: >you would include it as a nuisance variable in the glm >On Wed, 22 Nov 2017,

Re: [Freesurfer] LGI

erely, Zheng At 2017-11-27 11:54:33, "Douglas Greve" wrote: yes, that should work too On 11/26/17 8:38 PM, 郑凤莲 wrote: Hi Greve, Tnahks for your reply. I used "mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.

Re: [Freesurfer] Qdec

I get it. Thank you very much. Best, Zheng At 2017-11-27 11:46:46, "Bruce Fischl" wrote: It’s because people have found empirically that surface area and volume are correlated with TIV, but thickness is not cheers Bruce On Nov 26, 2017, at 9:54 PM, 郑凤莲 <13181786...@163.com

Re: [Freesurfer] Qdec

Hi Bruce, Thanks for your help. But I have a doubt in why we should do in this way? Are there any principles or mechanisms in Qdec? Sincerely, Zheng At 2017-11-27 10:47:49, "Bruce Fischl" wrote: Yes On Nov 26, 2017, at 9:40 PM, 郑凤莲 <13181786...@163.com> w

Re: [Freesurfer] Qdec

Hi Bruce, That is, I should set eTIV at Nuisance Factors for volume and surface area, not for thickness in qdec, is it right? At 2017-11-27 10:22:05, "Bruce Fischl" wrote: >you should correct for eTIV for volume (but not for thickness) >On Mon, 27 >Nov 2017, 郑凤莲 w

Re: [Freesurfer] Qdec

Hi Greve, Only for age and surface area, no thickness or volume, is it right? Thanks! Zheng At 2017-11-26 03:04:26, "Douglas Greve" wrote: Yes, for age and surface area. On 11/23/17 2:05 AM, 郑凤莲 wrote: Hi professors, I am using Qdec in Freesurfer. I want to

Re: [Freesurfer] LGI

ctab subject lh white In the output, the mean LGI will be under the "ThickAvg" column On 11/23/17 1:58 AM, 郑凤莲 wrote: Hi experts, I am using Freesurfer 6.0 for LGI. I ran recon-all and got the map of LGI. My question is that can I get the specific value of every gyrus a

[Freesurfer] Qdec

Hi professors, I am using Qdec in Freesurfer. I want to study the relationships between age and cortical thickness, age and cortical volume, age and surface area. Is it necessary to corrected by eTIV for volume and surface area in Qdec? I am looking forward to your reply. Thanks, Z

[Freesurfer] LGI

Hi experts, I am using Freesurfer 6.0 for LGI. I ran recon-all and got the map of LGI. My question is that can I get the specific value of every gyrus as the value of thickness in the file of lh.aparc.stats? I can't find it from stats direction. Thanks a lot ! Zheng__

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, It's OK. Thank you very much for your reply ! I will find it in other way. Sincerely, Zheng At 2017-11-23 11:37:37, "Bruce Fischl" wrote: Sorry, I don’t remember. You can search on the wiki or maybe someone else will chime in Bruce On Nov 22, 2017, at 8:30 PM

Re: [Freesurfer]  hippocampus subfields

ncluded sulcal CSF. I think we include a whole brain volume in the >aseg.stats file that you can use, although I don't remember what it's >called > >cheers >Bruce >On Wed, 22 Nov 2017, 郑凤莲 wrote: > >> Hi Bruce, >> Thank you very much. I will try it. And I

Re: [Freesurfer]  hippocampus subfields

what it's >called > >cheers >Bruce >On Wed, 22 Nov 2017, 郑凤莲 wrote: > >> Hi Bruce, >> Thank you very much. I will try it. And I have another question. I also >> want to study the >> relation between age and the whole brain volume, gray matter

Re: [Freesurfer]  hippocampus subfields

:43, "Bruce Fischl" wrote: >you would include it as a nuisance variable in the glm >On Wed, 22 Nov 2017, >郑凤莲 wrote: > >> Hi Bruce, >> >> Thanks for your quick reply. These results are not correted by eTIV, If >> eTIV are corrected, I >> ca

Re: [Freesurfer]  hippocampus subfields

11-22 10:14:16，"Bruce Fischl" 写道： >is this eTIV corrected? I would look at some of the outliers and make >sure that the segmentations are accurate. Certainly the trend is in the >correct (and depressing) direction. > >cheers >Bruce >On Wed, 22 Nov 2017, 郑凤莲 wrote:

Re: [Freesurfer]  hippocampus subfields

wrote: >Hi Zheng > >I would scatter plot age vs. volume, coloring men and women differently >(or different symbols) with and without eTIV correction to get an idea of >what is going on > >cheers >Bruce > > >On Mon, 20 Nov >2017, 郑凤莲 wrote: > >> Hi

Re: [Freesurfer] TRACULA

. Sincerely, Zheng At 2017-11-01 21:59:11, "Yendiki, Anastasia" wrote: Hi Zheng - I'll need the trac-all.log file, the gradient table, and the b-value table. Please do not send other data at the moment. Thanks, Anastasia. From: 郑凤莲 <13181786...@163.com> Sent: Tuesday, Oct

Re: [Freesurfer]  hippocampus subfields

quot;Bruce Fischl" wrote: >Hi Zheng > >how uniform is your distribution? I'm hardly an expert on this, but I >wouldn't expect very large effects until you get into the older end of >that range. Have you scatter plotted your data? >Bruce >On Mon, 20 Nov 2017, 郑凤莲 &

Re: [Freesurfer]  hippocampus subfields

correcting for eTIV? What measure are you comparing? > >cheers >Bruce > On Sun, 19 Nov 2017, 郑凤莲 wrote: > >> Hi Bruce, >> >> I am sorry for this situation. >> In the first way, there was an statistical difference in left >> hippocampus, but no di

Re: [Freesurfer]  hippocampus subfields

this result. Can you understand me this time? Thanks, Zheng At 2017-11-18 22:58:56, "Bruce Fischl" wrote: >Hi Zheng > >no difference between what and what? > >cheers >Bruce >On Fri, 17 Nov 2017, 郑凤莲 wrote: > >> Hi professor, >> &g

[Freesurfer] eTIV as a covariate

Hi Professor, I ran three steps of "recon-all" and get the cortical thickness, surfarea, GrayVol in lh.aparc.stats and subcotical volume in aseg.stats. If I want to use SPSS software for statistics， should I use eTIV as a covariate for everyone? Thank you very much. Sincerely, Zheng ___

[Freesurfer] (无主题)

Hi Professor, I ran three steps of "recon-all" and get the cortical thickness, surfarea, GrayVol in lh.aparc.stats and subcotical volume in aseg.stats. If I want to use SPSS software for statistics. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harva

Re: [Freesurfer] hippocampus subfields

volume? What is the age range? -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of 郑凤莲 <13181786...@163.com> Reply-To: Freesurfer support list Date:

Re: [Freesurfer] hippocampus subfields

Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of 郑凤莲 <13181786...@163.com> Reply-To: Freesurfer support list Date: Friday, 17 November 2017 at 0

[Freesurfer] hippocampus subfields

Hi professor, I am using Freesurfer for DTI data. When I run 'mri_segstats', I got the result that there was anobvious difference in left hippocampus, but no difference in right hippocampus. Then, I run segmentation of hippocampus subfields.The result showed there is no difference in tota

[Freesurfer]  hippocampus subfields

Hi professor, I am using Freesurfer for DTI data. When I run 'mri_segstats', I got the result that there was an obvious difference in left hippocampus, but no difference in right hippocampus. Then, I run segmentation of hippocampus subfields. The result showed there is no difference in to

Re: [Freesurfer] Recons for Allen Brain Institute T1 images with v5.3 online

Hi Melanie, I don't understand what you mean. Could you tell me what I am going to do to solve my problem? Thanks, Zheng At 2017-10-30 16:33:02, "Melanie Ganz" wrote: Hi, So here’s the Wiki page for the human Allen brain data recons: https://surfer.nmr.mgh.harvard.edu/fswiki

[Freesurfer] dmrirc_v1

Hi Professor， Thank you for publishing Freesurfer software. Now I am studying DTI using Freesurfer. And I am interested in the technology of TRACULA. But when I run it, I encountered an error about valid frame numbers, as shown in the picture. And there is my dmrirc file. Do you know which pa

[Freesurfer] dmrirc_v1

Hi Professor， Thank you for publishing Freesurfer software. Now I am studying DTI using Freesurfer. And I am interested in the technology of TRACULA. But when I run it, I encountered an error about valid frame numbers, as shown in the picture. And there is my dmrirc file. Do you know which pa